diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index aaffe5ecc9..2b323c0272 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -37,10 +37,15 @@ from typing import (
 import attr
 
 from synapse.config.homeserver import HomeServerConfig
-from synapse.storage.database import LoggingDatabaseConnection, LoggingTransaction
+from synapse.storage.database import (
+    DatabasePool,
+    LoggingDatabaseConnection,
+    LoggingTransaction,
+)
 from synapse.storage.engines import BaseDatabaseEngine, PostgresEngine, Sqlite3Engine
 from synapse.storage.schema import SCHEMA_COMPAT_VERSION, SCHEMA_VERSION
 from synapse.storage.types import Cursor
+from synapse.util.iterutils import batch_iter
 
 logger = logging.getLogger(__name__)
 
@@ -567,6 +572,161 @@ def _upgrade_existing_database(
 
     logger.info("Schema now up to date")
 
+    # FIXME: This can be removed once we bump `SCHEMA_COMPAT_VERSION` and run the
+    # foreground update for
+    # `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` (tracked by
+    # https://github.com/element-hq/synapse/issues/TODO)
+    _clear_out_of_date_sliding_sync_tables(
+        txn=cur,
+    )
+
+
+def _clear_out_of_date_sliding_sync_tables(
+    txn: LoggingTransaction,
+) -> None:
+    """
+    Clears out-of-date entries from the
+    `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` tables.
+
+    This accounts for when someone downgrades their Synapse version and then upgrades it
+    again. This will ensure that we don't have any out-of-date data in the
+    `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` tables.
+
+    FIXME: This can be removed once we bump `SCHEMA_COMPAT_VERSION` and run the
+    foreground update for
+    `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` (tracked by
+    https://github.com/element-hq/synapse/issues/TODO)
+    """
+
+    _clear_out_of_date_sliding_sync_joined_rooms_table(txn)
+    _clear_out_of_date_sliding_sync_membership_snapshots_table(txn)
+
+
+def _clear_out_of_date_sliding_sync_joined_rooms_table(
+    txn: LoggingTransaction,
+) -> None:
+    """
+    Clears out-of-date entries from the `sliding_sync_joined_rooms` table.
+
+    This accounts for when someone downgrades their Synapse version and then upgrades it
+    again. This will ensure that we don't have any out-of-date data in the
+    `sliding_sync_joined_rooms` table.
+
+    FIXME: This can be removed once we bump `SCHEMA_COMPAT_VERSION` and run the
+    foreground update for
+    `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` (tracked by
+    https://github.com/element-hq/synapse/issues/TODO)
+    """
+
+    # Find the point when we stopped writing to the `sliding_sync_joined_rooms` table
+    txn.execute(
+        """
+        SELECT event_stream_ordering
+        FROM sliding_sync_joined_rooms
+        ORDER BY event_stream_ordering DESC
+        LIMIT 1
+        """,
+    )
+
+    row = txn.fetchone()
+    # We have nothing written to the `sliding_sync_joined_rooms` table so there is
+    # nothing to clean up
+    if row is None:
+        return
+
+    max_stream_ordering_sliding_sync_joined_rooms_table = row[0]
+
+    txn.execute(
+        """
+        SELECT DISTINCT(room_id)
+        FROM events
+        WHERE stream_ordering > ?
+        ORDER BY stream_ordering DESC
+        """,
+        (max_stream_ordering_sliding_sync_joined_rooms_table,),
+    )
+
+    room_rows = txn.fetchall()
+    # No new events have been written to the `events` table since the last time we wrote
+    # to the `sliding_sync_joined_rooms` table so there is nothing to clean up. This is
+    # the expected normal scenario for people who have not downgraded their Synapse
+    # version.
+    if not room_rows:
+        return
+
+    for chunk in batch_iter(room_rows, 1000):
+        # Handle updating the `sliding_sync_joined_rooms` table
+        #
+        DatabasePool.simple_delete_many_batch_txn(
+            txn,
+            table="sliding_sync_joined_rooms",
+            keys=("room_id",),
+            values=chunk,
+        )
+
+
+def _clear_out_of_date_sliding_sync_membership_snapshots_table(
+    txn: LoggingTransaction,
+) -> None:
+    """
+    Clears out-of-date entries from the `sliding_sync_membership_snapshots` table.
+
+    This accounts for when someone downgrades their Synapse version and then upgrades it
+    again. This will ensure that we don't have any out-of-date data in the
+    `sliding_sync_membership_snapshots` table.
+
+    FIXME: This can be removed once we bump `SCHEMA_COMPAT_VERSION` and run the
+    foreground update for
+    `sliding_sync_joined_rooms`/`sliding_sync_membership_snapshots` (tracked by
+    https://github.com/element-hq/synapse/issues/TODO)
+    """
+
+    # Find the point when we stopped writing to the `sliding_sync_membership_snapshots` table
+    txn.execute(
+        """
+        SELECT event_stream_ordering
+        FROM sliding_sync_membership_snapshots
+        ORDER BY event_stream_ordering DESC
+        LIMIT 1
+        """,
+    )
+
+    row = txn.fetchone()
+    # We have nothing written to the `sliding_sync_membership_snapshots` table so there is
+    # nothing to clean up
+    if row is None:
+        return
+
+    max_stream_ordering_sliding_sync_membership_snapshots_table = row[0]
+
+    txn.execute(
+        """
+        SELECT DISTINCT(user_id, room_id)
+        FROM room_memberships
+        WHERE event_stream_ordering > ?
+        ORDER BY event_stream_ordering DESC
+        """,
+        (max_stream_ordering_sliding_sync_membership_snapshots_table,),
+    )
+
+    membership_rows = txn.fetchall()
+    # No new events have been written to the `events` table since the last time we wrote
+    # to the `sliding_sync_membership_snapshots` table so there is nothing to clean up.
+    # This is the expected normal scenario for people who have not downgraded their
+    # Synapse version.
+    if not membership_rows:
+        return
+
+    for chunk in batch_iter(membership_rows, 1000):
+        # Handle updating the `sliding_sync_membership_snapshots` table
+        #
+        DatabasePool.simple_delete_many_batch_txn(
+            txn,
+            table="sliding_sync_membership_snapshots",
+            keys=("user_id", "room_id"),
+            values=chunk,
+        )
+
 
 def _apply_module_schemas(
     txn: Cursor, database_engine: BaseDatabaseEngine, config: HomeServerConfig