diff --git a/changelog.d/1172.misc b/changelog.d/1172.misc
new file mode 100644
index 000000000..30b3e5608
--- /dev/null
+++ b/changelog.d/1172.misc
@@ -0,0 +1 @@
+Update `user_filters` table to have a unique index, and non-null columns. Thanks to @pik for contributing this.
\ No newline at end of file
diff --git a/synapse/storage/schema/delta/56/unique_user_filter_index.py b/synapse/storage/schema/delta/56/unique_user_filter_index.py
new file mode 100644
index 000000000..4efc1a586
--- /dev/null
+++ b/synapse/storage/schema/delta/56/unique_user_filter_index.py
@@ -0,0 +1,46 @@
+import logging
+
+from synapse.storage.engines import PostgresEngine
+
+logger = logging.getLogger(__name__)
+
+
+def run_upgrade(cur, database_engine, *args, **kwargs):
+    if isinstance(database_engine, PostgresEngine):
+        select_clause = """
+        CREATE TEMPORARY TABLE user_filters_migration AS
+            SELECT DISTINCT ON (user_id, filter_id) user_id, filter_id, filter_json
+            FROM user_filters;
+        """
+    else:
+        select_clause = """
+        CREATE TEMPORARY TABLE user_filters_migration AS
+            SELECT * FROM user_filters GROUP BY user_id, filter_id;
+        """
+    sql = (
+        """
+        BEGIN;
+            %s
+            DROP INDEX user_filters_by_user_id_filter_id;
+            DELETE FROM user_filters;
+            ALTER TABLE user_filters
+               ALTER COLUMN user_id SET NOT NULL
+               ALTER COLUMN filter_id SET NOT NULL
+               ALTER COLUMN filter_json SET NOT NULL;
+            INSERT INTO user_filters(user_id, filter_id, filter_json)
+                SELECT * FROM user_filters_migration;
+            DROP TABLE user_filters_migration;
+            CREATE UNIQUE INDEX user_filters_by_user_id_filter_id_unique
+                ON user_filters(user_id, filter_id);
+        END;
+    """
+        % select_clause
+    )
+    if isinstance(database_engine, PostgresEngine):
+        cur.execute(sql)
+    else:
+        cur.executescript(sql)
+
+
+def run_create(cur, database_engine, *args, **kwargs):
+    pass