diff --git a/scripts/upgrade_appservice_db.py b/scripts/upgrade_appservice_db.py
deleted file mode 100644
index ae1b91c64..000000000
--- a/scripts/upgrade_appservice_db.py
+++ /dev/null
@@ -1,54 +0,0 @@
-from synapse.storage import read_schema
-import argparse
-import json
-import sqlite3
-
-
-def do_other_deltas(cursor):
-    cursor.execute("PRAGMA user_version")
-    row = cursor.fetchone()
-
-    if row and row[0]:
-        user_version = row[0]
-        # Run every version since after the current version.
-        for v in range(user_version + 1, 10):
-            print "Running delta: %d" % (v,)
-            sql_script = read_schema("delta/v%d" % (v,))
-            cursor.executescript(sql_script)
-
-
-def update_app_service_table(cur):
-    cur.execute("SELECT id, regex FROM application_services_regex")
-    for row in cur.fetchall():
-        try:
-            print "checking %s..." % row[0]
-            json.loads(row[1])
-        except ValueError:
-            # row isn't in json, make it so.
-            string_regex = row[1]
-            new_regex = json.dumps({
-                "regex": string_regex,
-                "exclusive": True
-            })
-            cur.execute(
-                "UPDATE application_services_regex SET regex=? WHERE id=?",
-                (new_regex, row[0])
-            )
-
-
-def main(dbname):
-    con = sqlite3.connect(dbname)
-    cur = con.cursor()
-    do_other_deltas(cur)
-    update_app_service_table(cur)
-    cur.execute("PRAGMA user_version = 14")
-    cur.close()
-    con.commit()
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument("database")
-    args = parser.parse_args()
-
-    main(args.database)
diff --git a/synapse/app/homeserver.py b/synapse/app/homeserver.py
index 5695d5aff..b3ba7dfdd 100755
--- a/synapse/app/homeserver.py
+++ b/synapse/app/homeserver.py
@@ -17,7 +17,9 @@
 import sys
 sys.dont_write_bytecode = True
 
-from synapse.storage import prepare_database, UpgradeDatabaseException
+from synapse.storage import (
+    prepare_database, prepare_sqlite3_database, UpgradeDatabaseException,
+)
 
 from synapse.server import HomeServer
 
@@ -335,6 +337,7 @@ def setup():
 
     try:
         with sqlite3.connect(db_name) as db_conn:
+            prepare_sqlite3_database(db_conn)
             prepare_database(db_conn)
     except UpgradeDatabaseException:
         sys.stderr.write(
diff --git a/synapse/storage/__init__.py b/synapse/storage/__init__.py
index d6ec446bd..a3ff99569 100644
--- a/synapse/storage/__init__.py
+++ b/synapse/storage/__init__.py
@@ -45,35 +45,18 @@ from syutil.jsonutil import encode_canonical_json
 from synapse.crypto.event_signing import compute_event_reference_hash
 
 
+import fnmatch
+import imp
 import logging
 import os
+import re
 
 
 logger = logging.getLogger(__name__)
 
 
-SCHEMAS = [
-    "transactions",
-    "users",
-    "profiles",
-    "presence",
-    "im",
-    "room_aliases",
-    "keys",
-    "redactions",
-    "state",
-    "event_edges",
-    "event_signatures",
-    "pusher",
-    "media_repository",
-    "application_services",
-    "filtering",
-    "rejections",
-]
-
-
-# Remember to update this number every time an incompatible change is made to
-# database schema files, so the users will be informed on server restarts.
+# Remember to update this number every time a change is made to database
+# schema files, so the users will be informed on server restarts.
 SCHEMA_VERSION = 14
 
 dir_path = os.path.abspath(os.path.dirname(__file__))
@@ -576,28 +559,15 @@ class DataStore(RoomMemberStore, RoomStore,
         )
 
 
-def schema_path(schema):
-    """ Get a filesystem path for the named database schema
-
-    Args:
-        schema: Name of the database schema.
-    Returns:
-        A filesystem path pointing at a ".sql" file.
-
-    """
-    schemaPath = os.path.join(dir_path, "schema", schema + ".sql")
-    return schemaPath
-
-
-def read_schema(schema):
+def read_schema(path):
     """ Read the named database schema.
 
     Args:
-        schema: Name of the datbase schema.
+        path: Path of the database schema.
     Returns:
         A string containing the database schema.
     """
-    with open(schema_path(schema)) as schema_file:
+    with open(path) as schema_file:
         return schema_file.read()
 
 
@@ -610,49 +580,275 @@ class UpgradeDatabaseException(PrepareDatabaseException):
 
 
 def prepare_database(db_conn):
-    """ Set up all the dbs. Since all the *.sql have IF NOT EXISTS, so we
-    don't have to worry about overwriting existing content.
+    """Prepares a database for usage. Will either create all necessary tables
+    or upgrade from an older schema version.
     """
-    c = db_conn.cursor()
-    c.execute("PRAGMA user_version")
-    row = c.fetchone()
+    try:
+        cur = db_conn.cursor()
+        version_info = _get_or_create_schema_state(cur)
 
-    if row and row[0]:
-        user_version = row[0]
-
-        if user_version > SCHEMA_VERSION:
-            raise ValueError(
-                "Cannot use this database as it is too " +
-                "new for the server to understand"
-            )
-        elif user_version < SCHEMA_VERSION:
-            logger.info(
-                "Upgrading database from version %d",
-                user_version
-            )
-
-            # Run every version since after the current version.
-            for v in range(user_version + 1, SCHEMA_VERSION + 1):
-                if v in (10, 14,):
-                    raise UpgradeDatabaseException(
-                        "No delta for version 10"
-                    )
-                sql_script = read_schema("delta/v%d" % (v,))
-                c.executescript(sql_script)
-
-            db_conn.commit()
+        if version_info:
+            user_version, delta_files, upgraded = version_info
+            _upgrade_existing_database(cur, user_version, delta_files, upgraded)
         else:
-            logger.info("Database is at version %r", user_version)
+            _setup_new_database(cur)
 
-    else:
-        sql_script = "BEGIN TRANSACTION;\n"
-        for sql_loc in SCHEMAS:
-            logger.debug("Applying schema %r", sql_loc)
-            sql_script += read_schema(sql_loc)
-            sql_script += "\n"
-        sql_script += "COMMIT TRANSACTION;"
-        c.executescript(sql_script)
+        cur.execute("PRAGMA user_version = %d" % (SCHEMA_VERSION,))
+
+        cur.close()
         db_conn.commit()
-        c.execute("PRAGMA user_version = %d" % SCHEMA_VERSION)
+    except:
+        db_conn.rollback()
+        raise
 
-    c.close()
+
+def _setup_new_database(cur):
+    """Sets up the database by finding a base set of "full schemas" and then
+    applying any necessary deltas.
+
+    The "full_schemas" directory has subdirectories named after versions. This
+    function searches for the highest version less than or equal to
+    `SCHEMA_VERSION` and executes all .sql files in that directory.
+
+    The function will then apply all deltas for all versions after the base
+    version.
+
+    Example directory structure:
+
+        schema/
+            delta/
+                ...
+            full_schemas/
+                3/
+                    test.sql
+                    ...
+                11/
+                    foo.sql
+                    bar.sql
+                ...
+
+    In the example foo.sql and bar.sql would be run, and then any delta files
+    for versions strictly greater than 11.
+    """
+    current_dir = os.path.join(dir_path, "schema", "full_schemas")
+    directory_entries = os.listdir(current_dir)
+
+    valid_dirs = []
+    pattern = re.compile(r"^\d+(\.sql)?$")
+    for filename in directory_entries:
+        match = pattern.match(filename)
+        abs_path = os.path.join(current_dir, filename)
+        if match and os.path.isdir(abs_path):
+            ver = int(match.group(0))
+            if ver <= SCHEMA_VERSION:
+                valid_dirs.append((ver, abs_path))
+        else:
+            logger.warn("Unexpected entry in 'full_schemas': %s", filename)
+
+    if not valid_dirs:
+        raise PrepareDatabaseException(
+            "Could not find a suitable base set of full schemas"
+        )
+
+    max_current_ver, sql_dir = max(valid_dirs, key=lambda x: x[0])
+
+    logger.debug("Initialising schema v%d", max_current_ver)
+
+    directory_entries = os.listdir(sql_dir)
+
+    sql_script = "BEGIN TRANSACTION;\n"
+    for filename in fnmatch.filter(directory_entries, "*.sql"):
+        sql_loc = os.path.join(sql_dir, filename)
+        logger.debug("Applying schema %s", sql_loc)
+        sql_script += read_schema(sql_loc)
+        sql_script += "\n"
+    sql_script += "COMMIT TRANSACTION;"
+    cur.executescript(sql_script)
+
+    cur.execute(
+        "INSERT OR REPLACE INTO schema_version (version, upgraded)"
+        " VALUES (?,?)",
+        (max_current_ver, False)
+    )
+
+    _upgrade_existing_database(
+        cur,
+        current_version=max_current_ver,
+        applied_delta_files=[],
+        upgraded=False
+    )
+
+
+def _upgrade_existing_database(cur, current_version, applied_delta_files,
+                               upgraded):
+    """Upgrades an existing database.
+
+    Delta files can either be SQL stored in *.sql files, or python modules
+    in *.py.
+
+    There can be multiple delta files per version. Synapse will keep track of
+    which delta files have been applied, and will apply any that haven't been
+    even if there has been no version bump. This is useful for development
+    where orthogonal schema changes may happen on separate branches.
+
+    Different delta files for the same version *must* be orthogonal and give
+    the same result when applied in any order. No guarantees are made on the
+    order of execution of these scripts.
+
+    This is a no-op of current_version == SCHEMA_VERSION.
+
+    Example directory structure:
+
+        schema/
+            delta/
+                11/
+                    foo.sql
+                    ...
+                12/
+                    foo.sql
+                    bar.py
+                ...
+            full_schemas/
+                ...
+
+    In the example, if current_version is 11, then foo.sql will be run if and
+    only if `upgraded` is True. Then `foo.sql` and `bar.py` would be run in
+    some arbitrary order.
+
+    Args:
+        cur (Cursor)
+        current_version (int): The current version of the schema.
+        applied_delta_files (list): A list of deltas that have already been
+            applied.
+        upgraded (bool): Whether the current version was generated by having
+            applied deltas or from full schema file. If `True` the function
+            will never apply delta files for the given `current_version`, since
+            the current_version wasn't generated by applying those delta files.
+    """
+
+    if current_version > SCHEMA_VERSION:
+        raise ValueError(
+            "Cannot use this database as it is too " +
+            "new for the server to understand"
+        )
+
+    start_ver = current_version
+    if not upgraded:
+        start_ver += 1
+
+    for v in range(start_ver, SCHEMA_VERSION + 1):
+        logger.debug("Upgrading schema to v%d", v)
+
+        delta_dir = os.path.join(dir_path, "schema", "delta", str(v))
+
+        try:
+            directory_entries = os.listdir(delta_dir)
+        except OSError:
+            logger.exception("Could not open delta dir for version %d", v)
+            raise UpgradeDatabaseException(
+                "Could not open delta dir for version %d" % (v,)
+            )
+
+        directory_entries.sort()
+        for file_name in directory_entries:
+            relative_path = os.path.join(str(v), file_name)
+            if relative_path in applied_delta_files:
+                continue
+
+            absolute_path = os.path.join(
+                dir_path, "schema", "delta", relative_path,
+            )
+            root_name, ext = os.path.splitext(file_name)
+            if ext == ".py":
+                # This is a python upgrade module. We need to import into some
+                # package and then execute its `run_upgrade` function.
+                module_name = "synapse.storage.v%d_%s" % (
+                    v, root_name
+                )
+                with open(absolute_path) as python_file:
+                    module = imp.load_source(
+                        module_name, absolute_path, python_file
+                    )
+                logger.debug("Running script %s", relative_path)
+                module.run_upgrade(cur)
+            elif ext == ".sql":
+                # A plain old .sql file, just read and execute it
+                delta_schema = read_schema(absolute_path)
+                logger.debug("Applying schema %s", relative_path)
+                cur.executescript(delta_schema)
+            else:
+                # Not a valid delta file.
+                logger.warn(
+                    "Found directory entry that did not end in .py or"
+                    " .sql: %s",
+                    relative_path,
+                )
+                continue
+
+            # Mark as done.
+            cur.execute(
+                "INSERT INTO applied_schema_deltas (version, file)"
+                " VALUES (?,?)",
+                (v, relative_path)
+            )
+
+            cur.execute(
+                "INSERT OR REPLACE INTO schema_version (version, upgraded)"
+                " VALUES (?,?)",
+                (v, True)
+            )
+
+
+def _get_or_create_schema_state(txn):
+    schema_path = os.path.join(
+        dir_path, "schema", "schema_version.sql",
+    )
+    create_schema = read_schema(schema_path)
+    txn.executescript(create_schema)
+
+    txn.execute("SELECT version, upgraded FROM schema_version")
+    row = txn.fetchone()
+    current_version = int(row[0]) if row else None
+    upgraded = bool(row[1]) if row else None
+
+    if current_version:
+        txn.execute(
+            "SELECT file FROM applied_schema_deltas WHERE version >= ?",
+            (current_version,)
+        )
+        return current_version, txn.fetchall(), upgraded
+
+    return None
+
+
+def prepare_sqlite3_database(db_conn):
+    """This function should be called before `prepare_database` on sqlite3
+    databases.
+
+    Since we changed the way we store the current schema version and handle
+    updates to schemas, we need a way to upgrade from the old method to the
+    new. This only affects sqlite databases since they were the only ones
+    supported at the time.
+    """
+    with db_conn:
+        schema_path = os.path.join(
+            dir_path, "schema", "schema_version.sql",
+        )
+        create_schema = read_schema(schema_path)
+        db_conn.executescript(create_schema)
+
+        c = db_conn.execute("SELECT * FROM schema_version")
+        rows = c.fetchall()
+        c.close()
+
+        if not rows:
+            c = db_conn.execute("PRAGMA user_version")
+            row = c.fetchone()
+            c.close()
+
+            if row and row[0]:
+                db_conn.execute(
+                    "INSERT OR REPLACE INTO schema_version (version, upgraded)"
+                    " VALUES (?,?)",
+                    (row[0], False)
+                )
diff --git a/synapse/storage/schema/application_services.sql b/synapse/storage/schema/application_services.sql
deleted file mode 100644
index e491ad5ae..000000000
--- a/synapse/storage/schema/application_services.sql
+++ /dev/null
@@ -1,34 +0,0 @@
-/* Copyright 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-CREATE TABLE IF NOT EXISTS application_services(
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    url TEXT,
-    token TEXT,
-    hs_token TEXT,
-    sender TEXT,
-    UNIQUE(token) ON CONFLICT ROLLBACK
-);
-
-CREATE TABLE IF NOT EXISTS application_services_regex(
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    as_id INTEGER NOT NULL,
-    namespace INTEGER,  /* enum[room_id|room_alias|user_id] */
-    regex TEXT,
-    FOREIGN KEY(as_id) REFERENCES application_services(id)
-);
-
-
-
diff --git a/synapse/storage/schema/delta/v11.sql b/synapse/storage/schema/delta/11/v11.sql
similarity index 100%
rename from synapse/storage/schema/delta/v11.sql
rename to synapse/storage/schema/delta/11/v11.sql
diff --git a/synapse/storage/schema/delta/v12.sql b/synapse/storage/schema/delta/12/v12.sql
similarity index 100%
rename from synapse/storage/schema/delta/v12.sql
rename to synapse/storage/schema/delta/12/v12.sql
diff --git a/synapse/storage/schema/delta/v13.sql b/synapse/storage/schema/delta/13/v13.sql
similarity index 100%
rename from synapse/storage/schema/delta/v13.sql
rename to synapse/storage/schema/delta/13/v13.sql
diff --git a/synapse/storage/schema/delta/14/upgrade_appservice_db.py b/synapse/storage/schema/delta/14/upgrade_appservice_db.py
new file mode 100644
index 000000000..847b1c5b8
--- /dev/null
+++ b/synapse/storage/schema/delta/14/upgrade_appservice_db.py
@@ -0,0 +1,23 @@
+import json
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+def run_upgrade(cur):
+    cur.execute("SELECT id, regex FROM application_services_regex")
+    for row in cur.fetchall():
+        try:
+            logger.debug("Checking %s..." % row[0])
+            json.loads(row[1])
+        except ValueError:
+            # row isn't in json, make it so.
+            string_regex = row[1]
+            new_regex = json.dumps({
+                "regex": string_regex,
+                "exclusive": True
+            })
+            cur.execute(
+                "UPDATE application_services_regex SET regex=? WHERE id=?",
+                (new_regex, row[0])
+            )
diff --git a/synapse/storage/schema/delta/v2.sql b/synapse/storage/schema/delta/v2.sql
deleted file mode 100644
index f740f6dd5..000000000
--- a/synapse/storage/schema/delta/v2.sql
+++ /dev/null
@@ -1,168 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-CREATE TABLE IF NOT EXISTS events(
-    stream_ordering INTEGER PRIMARY KEY AUTOINCREMENT,
-    topological_ordering INTEGER NOT NULL,
-    event_id TEXT NOT NULL,
-    type TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    content TEXT NOT NULL,
-    unrecognized_keys TEXT,
-    processed BOOL NOT NULL,
-    outlier BOOL NOT NULL,
-    CONSTRAINT ev_uniq UNIQUE (event_id)
-);
-
-CREATE INDEX IF NOT EXISTS events_event_id ON events (event_id);
-CREATE INDEX IF NOT EXISTS events_stream_ordering ON events (stream_ordering);
-CREATE INDEX IF NOT EXISTS events_topological_ordering ON events (topological_ordering);
-CREATE INDEX IF NOT EXISTS events_room_id ON events (room_id);
-
-CREATE TABLE IF NOT EXISTS state_events(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    type TEXT NOT NULL,
-    state_key TEXT NOT NULL,
-    prev_state TEXT
-);
-
-CREATE UNIQUE INDEX IF NOT EXISTS state_events_event_id ON state_events (event_id);
-CREATE INDEX IF NOT EXISTS state_events_room_id ON state_events (room_id);
-CREATE INDEX IF NOT EXISTS state_events_type ON state_events (type);
-CREATE INDEX IF NOT EXISTS state_events_state_key ON state_events (state_key);
-
-
-CREATE TABLE IF NOT EXISTS current_state_events(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    type TEXT NOT NULL,
-    state_key TEXT NOT NULL,
-    CONSTRAINT curr_uniq UNIQUE (room_id, type, state_key) ON CONFLICT REPLACE
-);
-
-CREATE INDEX IF NOT EXISTS curr_events_event_id ON current_state_events (event_id);
-CREATE INDEX IF NOT EXISTS current_state_events_room_id ON current_state_events (room_id);
-CREATE INDEX IF NOT EXISTS current_state_events_type ON current_state_events (type);
-CREATE INDEX IF NOT EXISTS current_state_events_state_key ON current_state_events (state_key);
-
-CREATE TABLE IF NOT EXISTS room_memberships(
-    event_id TEXT NOT NULL,
-    user_id TEXT NOT NULL,
-    sender TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    membership TEXT NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS room_memberships_event_id ON room_memberships (event_id);
-CREATE INDEX IF NOT EXISTS room_memberships_room_id ON room_memberships (room_id);
-CREATE INDEX IF NOT EXISTS room_memberships_user_id ON room_memberships (user_id);
-
-CREATE TABLE IF NOT EXISTS feedback(
-    event_id TEXT NOT NULL,
-    feedback_type TEXT,
-    target_event_id TEXT,
-    sender TEXT,
-    room_id TEXT
-);
-
-CREATE TABLE IF NOT EXISTS topics(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    topic TEXT NOT NULL
-);
-
-CREATE TABLE IF NOT EXISTS room_names(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    name TEXT NOT NULL
-);
-
-CREATE TABLE IF NOT EXISTS rooms(
-    room_id TEXT PRIMARY KEY NOT NULL,
-    is_public INTEGER,
-    creator TEXT
-);
-
-CREATE TABLE IF NOT EXISTS room_join_rules(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    join_rule TEXT NOT NULL
-);
-CREATE INDEX IF NOT EXISTS room_join_rules_event_id ON room_join_rules(event_id);
-CREATE INDEX IF NOT EXISTS room_join_rules_room_id ON room_join_rules(room_id);
-
-
-CREATE TABLE IF NOT EXISTS room_power_levels(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    user_id TEXT NOT NULL,
-    level INTEGER NOT NULL
-);
-CREATE INDEX IF NOT EXISTS room_power_levels_event_id ON room_power_levels(event_id);
-CREATE INDEX IF NOT EXISTS room_power_levels_room_id ON room_power_levels(room_id);
-CREATE INDEX IF NOT EXISTS room_power_levels_room_user ON room_power_levels(room_id, user_id);
-
-
-CREATE TABLE IF NOT EXISTS room_default_levels(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    level INTEGER NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS room_default_levels_event_id ON room_default_levels(event_id);
-CREATE INDEX IF NOT EXISTS room_default_levels_room_id ON room_default_levels(room_id);
-
-
-CREATE TABLE IF NOT EXISTS room_add_state_levels(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    level INTEGER NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS room_add_state_levels_event_id ON room_add_state_levels(event_id);
-CREATE INDEX IF NOT EXISTS room_add_state_levels_room_id ON room_add_state_levels(room_id);
-
-
-CREATE TABLE IF NOT EXISTS room_send_event_levels(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    level INTEGER NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS room_send_event_levels_event_id ON room_send_event_levels(event_id);
-CREATE INDEX IF NOT EXISTS room_send_event_levels_room_id ON room_send_event_levels(room_id);
-
-
-CREATE TABLE IF NOT EXISTS room_ops_levels(
-    event_id TEXT NOT NULL,
-    room_id TEXT NOT NULL,
-    ban_level INTEGER,
-    kick_level INTEGER
-);
-
-CREATE INDEX IF NOT EXISTS room_ops_levels_event_id ON room_ops_levels(event_id);
-CREATE INDEX IF NOT EXISTS room_ops_levels_room_id ON room_ops_levels(room_id);
-
-
-CREATE TABLE IF NOT EXISTS room_hosts(
-    room_id TEXT NOT NULL,
-    host TEXT NOT NULL,
-    CONSTRAINT room_hosts_uniq UNIQUE (room_id, host) ON CONFLICT IGNORE
-);
-
-CREATE INDEX IF NOT EXISTS room_hosts_room_id ON room_hosts (room_id);
-
-PRAGMA user_version = 2;
diff --git a/synapse/storage/schema/delta/v3.sql b/synapse/storage/schema/delta/v3.sql
deleted file mode 100644
index c67e38ff5..000000000
--- a/synapse/storage/schema/delta/v3.sql
+++ /dev/null
@@ -1,27 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-
-CREATE INDEX IF NOT EXISTS room_aliases_alias ON room_aliases(room_alias);
-CREATE INDEX IF NOT EXISTS room_aliases_id ON room_aliases(room_id);
-
-
-CREATE INDEX IF NOT EXISTS room_alias_servers_alias ON room_alias_servers(room_alias);
-
-DELETE FROM room_aliases WHERE rowid NOT IN (SELECT max(rowid) FROM room_aliases GROUP BY room_alias, room_id);
-
-CREATE UNIQUE INDEX IF NOT EXISTS room_aliases_uniq ON room_aliases(room_alias, room_id);
-
-PRAGMA user_version = 3;
diff --git a/synapse/storage/schema/delta/v4.sql b/synapse/storage/schema/delta/v4.sql
deleted file mode 100644
index d3807b768..000000000
--- a/synapse/storage/schema/delta/v4.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-CREATE TABLE IF NOT EXISTS redactions (
-    event_id TEXT NOT NULL,
-    redacts TEXT NOT NULL,
-    CONSTRAINT ev_uniq UNIQUE (event_id)
-);
-
-CREATE INDEX IF NOT EXISTS redactions_event_id ON redactions (event_id);
-CREATE INDEX IF NOT EXISTS redactions_redacts ON redactions (redacts);
-
-ALTER TABLE room_ops_levels ADD COLUMN redact_level INTEGER;
-
-PRAGMA user_version = 4;
diff --git a/synapse/storage/schema/delta/v5.sql b/synapse/storage/schema/delta/v5.sql
deleted file mode 100644
index 0874a1543..000000000
--- a/synapse/storage/schema/delta/v5.sql
+++ /dev/null
@@ -1,30 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-CREATE TABLE IF NOT EXISTS user_ips (
-    user TEXT NOT NULL,
-    access_token TEXT NOT NULL,
-    device_id TEXT,
-    ip TEXT NOT NULL,
-    user_agent TEXT NOT NULL,
-    last_seen INTEGER NOT NULL,
-    CONSTRAINT user_ip UNIQUE (user, access_token, ip, user_agent) ON CONFLICT REPLACE
-);
-
-CREATE INDEX IF NOT EXISTS user_ips_user ON user_ips(user);
-
-ALTER TABLE users ADD COLUMN admin BOOL DEFAULT 0 NOT NULL;
-
-PRAGMA user_version = 5;
diff --git a/synapse/storage/schema/delta/v6.sql b/synapse/storage/schema/delta/v6.sql
deleted file mode 100644
index a9e0a4fe0..000000000
--- a/synapse/storage/schema/delta/v6.sql
+++ /dev/null
@@ -1,31 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-CREATE TABLE IF NOT EXISTS server_tls_certificates(
-  server_name TEXT, -- Server name.
-  fingerprint TEXT, -- Certificate fingerprint.
-  from_server TEXT, -- Which key server the certificate was fetched from.
-  ts_added_ms INTEGER, -- When the certifcate was added.
-  tls_certificate BLOB, -- DER encoded x509 certificate.
-  CONSTRAINT uniqueness UNIQUE (server_name, fingerprint)
-);
-
-CREATE TABLE IF NOT EXISTS server_signature_keys(
-  server_name TEXT, -- Server name.
-  key_id TEXT, -- Key version.
-  from_server TEXT, -- Which key server the key was fetched form.
-  ts_added_ms INTEGER, -- When the key was added.
-  verify_key BLOB, -- NACL verification key.
-  CONSTRAINT uniqueness UNIQUE (server_name, key_id)
-);
diff --git a/synapse/storage/schema/delta/v8.sql b/synapse/storage/schema/delta/v8.sql
deleted file mode 100644
index 1e9f8b18c..000000000
--- a/synapse/storage/schema/delta/v8.sql
+++ /dev/null
@@ -1,34 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
- CREATE TABLE IF NOT EXISTS event_signatures_2 (
-    event_id TEXT,
-    signature_name TEXT,
-    key_id TEXT,
-    signature BLOB,
-    CONSTRAINT uniqueness UNIQUE (event_id, signature_name, key_id)
-);
-
-INSERT INTO event_signatures_2 (event_id, signature_name, key_id, signature)
-SELECT event_id, signature_name, key_id, signature FROM event_signatures;
-
-DROP TABLE event_signatures;
-ALTER TABLE event_signatures_2 RENAME TO event_signatures;
-
-CREATE INDEX IF NOT EXISTS event_signatures_id ON event_signatures (
-    event_id
-);
-
-PRAGMA user_version = 8;
\ No newline at end of file
diff --git a/synapse/storage/schema/delta/v9.sql b/synapse/storage/schema/delta/v9.sql
deleted file mode 100644
index 455d51a70..000000000
--- a/synapse/storage/schema/delta/v9.sql
+++ /dev/null
@@ -1,79 +0,0 @@
-/* Copyright 2014, 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
--- To track destination health
-CREATE TABLE IF NOT EXISTS destinations(
-    destination TEXT PRIMARY KEY,
-    retry_last_ts INTEGER,
-    retry_interval INTEGER
-);
-
-
-CREATE TABLE IF NOT EXISTS local_media_repository (
-    media_id TEXT, -- The id used to refer to the media.
-    media_type TEXT, -- The MIME-type of the media.
-    media_length INTEGER, -- Length of the media in bytes.
-    created_ts INTEGER, -- When the content was uploaded in ms.
-    upload_name TEXT, -- The name the media was uploaded with.
-    user_id TEXT, -- The user who uploaded the file.
-    CONSTRAINT uniqueness UNIQUE (media_id)
-);
-
-CREATE TABLE IF NOT EXISTS local_media_repository_thumbnails (
-    media_id TEXT, -- The id used to refer to the media.
-    thumbnail_width INTEGER, -- The width of the thumbnail in pixels.
-    thumbnail_height INTEGER, -- The height of the thumbnail in pixels.
-    thumbnail_type TEXT, -- The MIME-type of the thumbnail.
-    thumbnail_method TEXT, -- The method used to make the thumbnail.
-    thumbnail_length INTEGER, -- The length of the thumbnail in bytes.
-    CONSTRAINT uniqueness UNIQUE (
-        media_id, thumbnail_width, thumbnail_height, thumbnail_type
-    )
-);
-
-CREATE INDEX IF NOT EXISTS local_media_repository_thumbnails_media_id
-    ON local_media_repository_thumbnails (media_id);
-
-CREATE TABLE IF NOT EXISTS remote_media_cache (
-    media_origin TEXT, -- The remote HS the media came from.
-    media_id TEXT, -- The id used to refer to the media on that server.
-    media_type TEXT, -- The MIME-type of the media.
-    created_ts INTEGER, -- When the content was uploaded in ms.
-    upload_name TEXT, -- The name the media was uploaded with.
-    media_length INTEGER, -- Length of the media in bytes.
-    filesystem_id TEXT, -- The name used to store the media on disk.
-    CONSTRAINT uniqueness UNIQUE (media_origin, media_id)
-);
-
-CREATE TABLE IF NOT EXISTS remote_media_cache_thumbnails (
-    media_origin TEXT, -- The remote HS the media came from.
-    media_id TEXT, -- The id used to refer to the media.
-    thumbnail_width INTEGER, -- The width of the thumbnail in pixels.
-    thumbnail_height INTEGER, -- The height of the thumbnail in pixels.
-    thumbnail_method TEXT, -- The method used to make the thumbnail
-    thumbnail_type TEXT, -- The MIME-type of the thumbnail.
-    thumbnail_length INTEGER, -- The length of the thumbnail in bytes.
-    filesystem_id TEXT, -- The name used to store the media on disk.
-    CONSTRAINT uniqueness UNIQUE (
-        media_origin, media_id, thumbnail_width, thumbnail_height,
-        thumbnail_type, thumbnail_type
-    )
-);
-
-CREATE INDEX IF NOT EXISTS remote_media_cache_thumbnails_media_id
-    ON local_media_repository_thumbnails (media_id);
-
-
-PRAGMA user_version = 9;
diff --git a/synapse/storage/schema/filtering.sql b/synapse/storage/schema/filtering.sql
deleted file mode 100644
index beb39ca20..000000000
--- a/synapse/storage/schema/filtering.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/* Copyright 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-CREATE TABLE IF NOT EXISTS user_filters(
-  user_id TEXT,
-  filter_id INTEGER,
-  filter_json TEXT,
-  FOREIGN KEY(user_id) REFERENCES users(id)
-);
-
-CREATE INDEX IF NOT EXISTS user_filters_by_user_id_filter_id ON user_filters(
-  user_id, filter_id
-);
diff --git a/synapse/storage/schema/event_edges.sql b/synapse/storage/schema/full_schemas/11/event_edges.sql
similarity index 100%
rename from synapse/storage/schema/event_edges.sql
rename to synapse/storage/schema/full_schemas/11/event_edges.sql
diff --git a/synapse/storage/schema/event_signatures.sql b/synapse/storage/schema/full_schemas/11/event_signatures.sql
similarity index 100%
rename from synapse/storage/schema/event_signatures.sql
rename to synapse/storage/schema/full_schemas/11/event_signatures.sql
diff --git a/synapse/storage/schema/im.sql b/synapse/storage/schema/full_schemas/11/im.sql
similarity index 100%
rename from synapse/storage/schema/im.sql
rename to synapse/storage/schema/full_schemas/11/im.sql
diff --git a/synapse/storage/schema/keys.sql b/synapse/storage/schema/full_schemas/11/keys.sql
similarity index 100%
rename from synapse/storage/schema/keys.sql
rename to synapse/storage/schema/full_schemas/11/keys.sql
diff --git a/synapse/storage/schema/media_repository.sql b/synapse/storage/schema/full_schemas/11/media_repository.sql
similarity index 100%
rename from synapse/storage/schema/media_repository.sql
rename to synapse/storage/schema/full_schemas/11/media_repository.sql
diff --git a/synapse/storage/schema/presence.sql b/synapse/storage/schema/full_schemas/11/presence.sql
similarity index 100%
rename from synapse/storage/schema/presence.sql
rename to synapse/storage/schema/full_schemas/11/presence.sql
diff --git a/synapse/storage/schema/profiles.sql b/synapse/storage/schema/full_schemas/11/profiles.sql
similarity index 100%
rename from synapse/storage/schema/profiles.sql
rename to synapse/storage/schema/full_schemas/11/profiles.sql
diff --git a/synapse/storage/schema/redactions.sql b/synapse/storage/schema/full_schemas/11/redactions.sql
similarity index 100%
rename from synapse/storage/schema/redactions.sql
rename to synapse/storage/schema/full_schemas/11/redactions.sql
diff --git a/synapse/storage/schema/room_aliases.sql b/synapse/storage/schema/full_schemas/11/room_aliases.sql
similarity index 100%
rename from synapse/storage/schema/room_aliases.sql
rename to synapse/storage/schema/full_schemas/11/room_aliases.sql
diff --git a/synapse/storage/schema/state.sql b/synapse/storage/schema/full_schemas/11/state.sql
similarity index 100%
rename from synapse/storage/schema/state.sql
rename to synapse/storage/schema/full_schemas/11/state.sql
diff --git a/synapse/storage/schema/transactions.sql b/synapse/storage/schema/full_schemas/11/transactions.sql
similarity index 100%
rename from synapse/storage/schema/transactions.sql
rename to synapse/storage/schema/full_schemas/11/transactions.sql
diff --git a/synapse/storage/schema/users.sql b/synapse/storage/schema/full_schemas/11/users.sql
similarity index 100%
rename from synapse/storage/schema/users.sql
rename to synapse/storage/schema/full_schemas/11/users.sql
diff --git a/synapse/storage/schema/pusher.sql b/synapse/storage/schema/pusher.sql
deleted file mode 100644
index 3735b1154..000000000
--- a/synapse/storage/schema/pusher.sql
+++ /dev/null
@@ -1,46 +0,0 @@
-/* Copyright 2014 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Push notification endpoints that users have configured
-CREATE TABLE IF NOT EXISTS pushers (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  user_name TEXT NOT NULL,
-  profile_tag varchar(32) NOT NULL,
-  kind varchar(8) NOT NULL,
-  app_id varchar(64) NOT NULL,
-  app_display_name varchar(64) NOT NULL,
-  device_display_name varchar(128) NOT NULL,
-  pushkey blob NOT NULL,
-  ts BIGINT NOT NULL,
-  lang varchar(8),
-  data blob,
-  last_token TEXT,
-  last_success BIGINT,
-  failing_since BIGINT,
-  FOREIGN KEY(user_name) REFERENCES users(name),
-  UNIQUE (app_id, pushkey)
-);
-
-CREATE TABLE IF NOT EXISTS push_rules (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  user_name TEXT NOT NULL,
-  rule_id TEXT NOT NULL,
-  priority_class TINYINT NOT NULL,
-  priority INTEGER NOT NULL DEFAULT 0,
-  conditions TEXT NOT NULL,
-  actions TEXT NOT NULL,
-  UNIQUE(user_name, rule_id)
-);
-
-CREATE INDEX IF NOT EXISTS push_rules_user_name on push_rules (user_name);
diff --git a/synapse/storage/schema/rejections.sql b/synapse/storage/schema/rejections.sql
deleted file mode 100644
index bd2a8b1bb..000000000
--- a/synapse/storage/schema/rejections.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-/* Copyright 2015 OpenMarket Ltd
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-CREATE TABLE IF NOT EXISTS rejections(
-    event_id TEXT NOT NULL,
-    reason TEXT NOT NULL,
-    last_check TEXT NOT NULL,
-    CONSTRAINT ev_id UNIQUE (event_id) ON CONFLICT REPLACE
-);
diff --git a/synapse/storage/schema/schema_version.sql b/synapse/storage/schema/schema_version.sql
new file mode 100644
index 000000000..0431e2d05
--- /dev/null
+++ b/synapse/storage/schema/schema_version.sql
@@ -0,0 +1,30 @@
+/* Copyright 2015 OpenMarket Ltd
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+CREATE TABLE IF NOT EXISTS schema_version(
+    Lock char(1) NOT NULL DEFAULT 'X',  -- Makes sure this table only has one row.
+    version INTEGER NOT NULL,
+    upgraded BOOL NOT NULL,  -- Whether we reached this version from an upgrade or an initial schema.
+    CONSTRAINT schema_version_lock_x CHECK (Lock='X')
+    CONSTRAINT schema_version_lock_uniq UNIQUE (Lock)
+);
+
+CREATE TABLE IF NOT EXISTS applied_schema_deltas(
+    version INTEGER NOT NULL,
+    file TEXT NOT NULL,
+    CONSTRAINT schema_deltas_ver_file UNIQUE (version, file) ON CONFLICT IGNORE
+);
+
+CREATE INDEX IF NOT EXISTS schema_deltas_ver ON applied_schema_deltas(version);