diff --git a/synapse/handlers/e2e_room_keys.py b/synapse/handlers/e2e_room_keys.py
index 5edb3cfe04..b6d302cd6b 100644
--- a/synapse/handlers/e2e_room_keys.py
+++ b/synapse/handlers/e2e_room_keys.py
@@ -138,7 +138,7 @@ class E2eRoomKeysHandler(object):
                 else:
                     raise
 
-            if version_info['version'] != version:
+            if str(version_info['version']) != version:
                 # Check that the version we're trying to upload actually exists
                 try:
                     version_info = yield self.store.get_e2e_room_keys_version_info(
diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index b364719312..bd740e1e45 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -25,7 +25,7 @@ logger = logging.getLogger(__name__)
 
 # 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 = 51
+SCHEMA_VERSION = 52
 
 dir_path = os.path.abspath(os.path.dirname(__file__))
 
diff --git a/synapse/storage/schema/delta/52/e2e_room_keys.sql b/synapse/storage/schema/delta/52/e2e_room_keys.sql
new file mode 100644
index 0000000000..754985187e
--- /dev/null
+++ b/synapse/storage/schema/delta/52/e2e_room_keys.sql
@@ -0,0 +1,53 @@
+/* Copyright 2018 New Vector 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.
+ */
+
+/* Change version column to an integer so we can do MAX() sensibly
+ */
+CREATE TABLE e2e_room_keys_versions_new (
+    user_id TEXT NOT NULL,
+    version BIGINT NOT NULL,
+    algorithm TEXT NOT NULL,
+    auth_data TEXT NOT NULL,
+    deleted SMALLINT DEFAULT 0 NOT NULL
+);
+
+INSERT INTO e2e_room_keys_versions_new
+    SELECT user_id, version, algorithm, auth_data, deleted FROM e2e_room_keys_versions;
+
+DROP TABLE e2e_room_keys_versions;
+ALTER TABLE e2e_room_keys_versions_new RENAME TO e2e_room_keys_versions;
+
+CREATE UNIQUE INDEX e2e_room_keys_versions_idx ON e2e_room_keys_versions(user_id, version);
+
+/* Change e2e_rooms_keys to match
+ */
+CREATE TABLE e2e_room_keys_new (
+    user_id TEXT NOT NULL,
+    room_id TEXT NOT NULL,
+    session_id TEXT NOT NULL,
+    version BIGINT NOT NULL,
+    first_message_index INT,
+    forwarded_count INT,
+    is_verified BOOLEAN,
+    session_data TEXT NOT NULL
+);
+
+INSERT INTO e2e_room_keys_new
+    SELECT user_id, room_id, session_id, version, first_message_index, forwarded_count, is_verified, session_data FROM e2e_room_keys;
+
+DROP TABLE e2e_room_keys;
+ALTER TABLE e2e_room_keys_new RENAME TO e2e_room_keys;
+
+CREATE UNIQUE INDEX e2e_room_keys_idx ON e2e_room_keys(user_id, room_id, session_id);