diff --git a/synapse/app/homeserver.py b/synapse/app/homeserver.py
index 9f81a857a..6d6c1f8e0 100644
--- a/synapse/app/homeserver.py
+++ b/synapse/app/homeserver.py
@@ -68,7 +68,7 @@ from synapse.rest.key.v2 import KeyApiV2Resource
 from synapse.rest.media.v0.content_repository import ContentRepoResource
 from synapse.rest.well_known import WellKnownResource
 from synapse.server import HomeServer
-from synapse.storage import DataStore, are_all_users_on_domain
+from synapse.storage import DataStore
 from synapse.storage.engines import IncorrectDatabaseSetup, create_engine
 from synapse.storage.prepare_database import UpgradeDatabaseException, prepare_database
 from synapse.util.caches import CACHE_SIZE_FACTOR
@@ -295,16 +295,6 @@ class SynapseHomeServer(HomeServer):
                 logger.warning("Unrecognized listener type: %s", listener["type"])
 
     def run_startup_checks(self, db_conn, database_engine):
-        all_users_native = are_all_users_on_domain(
-            db_conn.cursor(), database_engine, self.hostname
-        )
-        if not all_users_native:
-            quit_with_error(
-                "Found users in database not native to %s!\n"
-                "You cannot changed a synapse server_name after it's been configured"
-                % (self.hostname,)
-            )
-
         try:
             database_engine.check_database(db_conn.cursor())
         except IncorrectDatabaseSetup as e:
diff --git a/synapse/storage/__init__.py b/synapse/storage/__init__.py
index 8fb18203d..ec89f645d 100644
--- a/synapse/storage/__init__.py
+++ b/synapse/storage/__init__.py
@@ -49,15 +49,3 @@ class Storage(object):
         self.persistence = EventsPersistenceStorage(hs, stores)
         self.purge_events = PurgeEventsStorage(hs, stores)
         self.state = StateGroupStorage(hs, stores)
-
-
-def are_all_users_on_domain(txn, database_engine, domain):
-    sql = database_engine.convert_param_style(
-        "SELECT COUNT(*) FROM users WHERE name NOT LIKE ?"
-    )
-    pat = "%:" + domain
-    txn.execute(sql, (pat,))
-    num_not_matching = txn.fetchall()[0][0]
-    if num_not_matching == 0:
-        return True
-    return False
diff --git a/synapse/storage/data_stores/main/__init__.py b/synapse/storage/data_stores/main/__init__.py
index 7f5fd81bc..66f8a9f3a 100644
--- a/synapse/storage/data_stores/main/__init__.py
+++ b/synapse/storage/data_stores/main/__init__.py
@@ -115,7 +115,17 @@ class DataStore(
     def __init__(self, database: Database, db_conn, hs):
         self.hs = hs
         self._clock = hs.get_clock()
-        self.database_engine = hs.database_engine
+        self.database_engine = database.engine
+
+        all_users_native = are_all_users_on_domain(
+            db_conn.cursor(), database.engine, hs.hostname
+        )
+        if not all_users_native:
+            raise Exception(
+                "Found users in database not native to %s!\n"
+                "You cannot changed a synapse server_name after it's been configured"
+                % (self.hostname,)
+            )
 
         self._stream_id_gen = StreamIdGenerator(
             db_conn,
@@ -555,3 +565,15 @@ class DataStore(
             retcols=["name", "password_hash", "is_guest", "admin", "user_type"],
             desc="search_users",
         )
+
+
+def are_all_users_on_domain(txn, database_engine, domain):
+    sql = database_engine.convert_param_style(
+        "SELECT COUNT(*) FROM users WHERE name NOT LIKE ?"
+    )
+    pat = "%:" + domain
+    txn.execute(sql, (pat,))
+    num_not_matching = txn.fetchall()[0][0]
+    if num_not_matching == 0:
+        return True
+    return False