diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8a073953b6..3510c740e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@ AppEngine version, listed here to ease deployment and troubleshooting.
 ## Next Release (replace with git tag when deployed)
  * Bump runtimeVersion to `2025.06.03`.
  * Upgraded dartdoc to `8.3.4`.
+ * Note: started to delete all `Secret` entries in Datastore.
 
 ## `20250603t091500-all`
  * Bump runtimeVersion to `2025.06.02`.
diff --git a/app/lib/tool/backfill/backfill_new_fields.dart b/app/lib/tool/backfill/backfill_new_fields.dart
index 922c48785b..56ad50a98e 100644
--- a/app/lib/tool/backfill/backfill_new_fields.dart
+++ b/app/lib/tool/backfill/backfill_new_fields.dart
@@ -4,6 +4,7 @@
 
 import 'package:logging/logging.dart';
 import 'package:pub_dev/package/models.dart';
+import 'package:pub_dev/service/secret/models.dart';
 import 'package:pub_dev/shared/datastore.dart';
 
 final _logger = Logger('backfill_new_fields');
@@ -14,6 +15,9 @@ final _logger = Logger('backfill_new_fields');
 /// CHANGELOG.md must be updated with the new fields, and the next
 /// release could remove the backfill from here.
 Future<void> backfillNewFields() async {
+  _logger.info('Deleting Secret entries');
+  await dbService.deleteWithQuery(dbService.query<Secret>());
+
   _logger.info('Backfill admin deleted fields...');
   await for (final e in dbService.query<Package>().run()) {
     if (e.isAdminDeleted == null) {