diff --git a/packages/backend-core/src/db/couch/DatabaseImpl.ts b/packages/backend-core/src/db/couch/DatabaseImpl.ts
index 1fa1e50e7e..e7ee54316a 100644
--- a/packages/backend-core/src/db/couch/DatabaseImpl.ts
+++ b/packages/backend-core/src/db/couch/DatabaseImpl.ts
@@ -353,18 +353,15 @@ export class DatabaseImpl implements Database {
   }
 
   async destroy() {
+    if (env.SQS_SEARCH_ENABLE && (await this.exists(SQLITE_DESIGN_DOC_ID))) {
+      // delete the design document, then run the cleanup operation
+      const definition = await this.get<SQLiteDefinition>(SQLITE_DESIGN_DOC_ID)
+      // remove all tables - save the definition then trigger a cleanup
+      definition.sql.tables = {}
+      await this.put(definition)
+      await this.sqlDiskCleanup()
+    }
     try {
-      if (env.SQS_SEARCH_ENABLE) {
-        // delete the design document, then run the cleanup operation
-        try {
-          const definition = await this.get<SQLiteDefinition>(
-            SQLITE_DESIGN_DOC_ID
-          )
-          await this.remove(SQLITE_DESIGN_DOC_ID, definition._rev)
-        } finally {
-          await this.sqlDiskCleanup()
-        }
-      }
       return await this.nano().db.destroy(this.name)
     } catch (err: any) {
       // didn't exist, don't worry
diff --git a/packages/server/src/api/routes/tests/application.spec.ts b/packages/server/src/api/routes/tests/application.spec.ts
index 7f89a5cac2..13b7451a7e 100644
--- a/packages/server/src/api/routes/tests/application.spec.ts
+++ b/packages/server/src/api/routes/tests/application.spec.ts
@@ -334,6 +334,12 @@ describe("/applications", () => {
       expect(events.app.deleted).toHaveBeenCalledTimes(1)
       expect(events.app.unpublished).toHaveBeenCalledTimes(1)
     })
+
+    it("should be able to delete an app after SQS_SEARCH_ENABLE has been set but app hasn't been migrated", async () => {
+      await config.withCoreEnv({ SQS_SEARCH_ENABLE: "true" }, async () => {
+        await config.api.application.delete(app.appId)
+      })
+    })
   })
 
   describe("POST /api/applications/:appId/duplicate", () => {