diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index 0bb970a296..2e7753820e 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -97,7 +97,8 @@ def prepare_database(db_conn, database_engine, config):
 
 def _setup_new_database(cur, database_engine, data_stores):
     """Sets up the database by finding a base set of "full schemas" and then
-    applying any necessary deltas.
+    applying any necessary deltas, including schemas from the given data
+    stores.
 
     The "full_schemas" directory has subdirectories named after versions. This
     function searches for the highest version less than or equal to
@@ -122,6 +123,15 @@ def _setup_new_database(cur, database_engine, data_stores):
 
     In the example foo.sql and bar.sql would be run, and then any delta files
     for versions strictly greater than 11.
+
+    Note: we apply the full schemas and deltas from the top level `schema/`
+    folder as well those in the data stores specified.
+
+    Args:
+        cur (Cursor): a database cursor
+        database_engine (DatabaseEngine)
+        data_stores (list[str]): The names of the data stores to instantiate
+            on the given database.
     """
     current_dir = os.path.join(dir_path, "schema", "full_schemas")
     directory_entries = os.listdir(current_dir)
@@ -245,6 +255,10 @@ def _upgrade_existing_database(
     only if `upgraded` is True. Then `foo.sql` and `bar.py` would be run in
     some arbitrary order.
 
+    Note: we apply the delta files from the specified data stores as well as
+    those in the top-level schema. We apply all delta files across data stores
+    for a version before applying those in the next version.
+
     Args:
         cur (Cursor)
         current_version (int): The current version of the schema.
@@ -254,6 +268,14 @@ def _upgrade_existing_database(
             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.
+        database_engine (DatabaseEngine)
+        config (synapse.config.homeserver.HomeServerConfig|None):
+            application config, or None if we are connecting to an existing
+            database which we expect to be configured already
+        data_stores (list[str]): The names of the data stores to instantiate
+            on the given database.
+        is_empty (bool): Is this a blank database? I.e. do we need to run the
+            upgrade portions of the delta scripts.
     """
 
     if current_version > SCHEMA_VERSION:
@@ -305,21 +327,19 @@ def _upgrade_existing_database(
                 # Data stores can have empty entries for a given version delta.
                 pass
             except OSError:
-                logger.exception("Could not open delta dir for version %d", v)
                 raise UpgradeDatabaseException(
-                    "Could not open delta dir for version %d" % (v,)
+                    "Could not open delta dir for version %d: %s" % (v, directory)
                 )
 
-        if not directory_entries:
-            continue
-
+        # We sort to ensure that we apply the delta files in a consistent
+        # order (to avoid bugs caused by inconsistent directory listing order)
         directory_entries.sort()
         for entry in directory_entries:
             file_name = entry.file_name
             relative_path = os.path.join(str(v), file_name)
             absolute_path = entry.absolute_path
 
-            logger.debug("Found file: %s", relative_path)
+            logger.debug("Found file: %s (%s)", relative_path, absolute_path)
             if relative_path in applied_delta_files:
                 continue
 
@@ -511,6 +531,9 @@ def _get_or_create_schema_state(txn, database_engine):
 class _DirectoryListing(object):
     """Helper class to store schema file name and the
     absolute path to it.
+
+    These entries get sorted, so for consistency we want to ensure that
+    `file_name` attr is kept first.
     """
 
     file_name = attr.ib()