diff --git a/.changeset/tender-months-count.md b/.changeset/tender-months-count.md
new file mode 100644
index 0000000000..9f76186409
--- /dev/null
+++ b/.changeset/tender-months-count.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-catalog-backend': patch
+---
+
+Skip deletion of bootstrap location when running the new catalog.
diff --git a/plugins/catalog-backend/migrationsv2/20210302150147_refresh_state.js b/plugins/catalog-backend/migrationsv2/20210302150147_refresh_state.js
index 2258017965..4e6cf4f282 100644
--- a/plugins/catalog-backend/migrationsv2/20210302150147_refresh_state.js
+++ b/plugins/catalog-backend/migrationsv2/20210302150147_refresh_state.js
@@ -191,11 +191,6 @@ exports.up = async function up(knex) {
     table.index(['key'], 'search_key_idx');
     table.index(['value'], 'search_value_idx');
   });
-
-  // Delete bootstrap location which is no longer required.
-  await knex('locations')
-    .where({ type: 'bootstrap', target: 'bootstrap' })
-    .delete();
 };
 
 /**