diff --git a/programs/local/LocalServer.cpp b/programs/local/LocalServer.cpp
index 571e3a3a4df..7d7fd8ff32d 100644
--- a/programs/local/LocalServer.cpp
+++ b/programs/local/LocalServer.cpp
@@ -654,8 +654,9 @@ void LocalServer::processConfig()
 
         if (!config().has("only-system-tables"))
         {
-            DatabaseCatalog::instance().startupBackgroundCleanup();
+            DatabaseCatalog::instance().createBackgroundTasks();
             loadMetadata(global_context);
+            DatabaseCatalog::instance().startupBackgroundCleanup();
         }
 
         /// For ClickHouse local if path is not set the loader will be disabled.
diff --git a/programs/server/Server.cpp b/programs/server/Server.cpp
index df223317fcc..34d266b6519 100644
--- a/programs/server/Server.cpp
+++ b/programs/server/Server.cpp
@@ -1656,11 +1656,12 @@ try
         /// that may execute DROP before loadMarkedAsDroppedTables() in background,
         /// and so loadMarkedAsDroppedTables() will find it and try to add, and UUID will overlap.
         database_catalog.loadMarkedAsDroppedTables();
-        database_catalog.startupBackgroundCleanup();
+        database_catalog.createBackgroundTasks();
         /// Then, load remaining databases
         loadMetadata(global_context, default_database);
         convertDatabasesEnginesIfNeed(global_context);
         startupSystemTables();
+        database_catalog.startupBackgroundCleanup();
         /// After loading validate that default database exists
         database_catalog.assertDatabaseExists(default_database);
         /// Load user-defined SQL functions.
diff --git a/src/Interpreters/DatabaseCatalog.cpp b/src/Interpreters/DatabaseCatalog.cpp
index 24d5f3491fd..6142608306f 100644
--- a/src/Interpreters/DatabaseCatalog.cpp
+++ b/src/Interpreters/DatabaseCatalog.cpp
@@ -152,20 +152,30 @@ void DatabaseCatalog::initializeAndLoadTemporaryDatabase()
     attachDatabase(TEMPORARY_DATABASE, db_for_temporary_and_external_tables);
 }
 
-void DatabaseCatalog::startupBackgroundCleanup()
+void DatabaseCatalog::createBackgroundTasks()
 {
+    /// It has to be done before databases are loaded (to avoid a race condition on initalization)
     if (Context::getGlobalContextInstance()->getApplicationType() == Context::ApplicationType::SERVER && unused_dir_cleanup_period_sec)
     {
         auto cleanup_task_holder
             = getContext()->getSchedulePool().createTask("DatabaseCatalog", [this]() { this->cleanupStoreDirectoryTask(); });
         cleanup_task = std::make_unique<BackgroundSchedulePoolTaskHolder>(std::move(cleanup_task_holder));
+    }
+
+    auto task_holder = getContext()->getSchedulePool().createTask("DatabaseCatalog", [this](){ this->dropTableDataTask(); });
+    drop_task = std::make_unique<BackgroundSchedulePoolTaskHolder>(std::move(task_holder));
+}
+
+void DatabaseCatalog::startupBackgroundCleanup()
+{
+    /// And it has to be done after all databases are loaded, otherwise cleanup_task may remove something that should not be removed
+    if (cleanup_task)
+    {
         (*cleanup_task)->activate();
         /// Do not start task immediately on server startup, it's not urgent.
         (*cleanup_task)->scheduleAfter(unused_dir_hide_timeout_sec * 1000);
     }
 
-    auto task_holder = getContext()->getSchedulePool().createTask("DatabaseCatalog", [this](){ this->dropTableDataTask(); });
-    drop_task = std::make_unique<BackgroundSchedulePoolTaskHolder>(std::move(task_holder));
     (*drop_task)->activate();
     std::lock_guard lock{tables_marked_dropped_mutex};
     if (!tables_marked_dropped.empty())
diff --git a/src/Interpreters/DatabaseCatalog.h b/src/Interpreters/DatabaseCatalog.h
index 5526e1496a3..11a855ebd79 100644
--- a/src/Interpreters/DatabaseCatalog.h
+++ b/src/Interpreters/DatabaseCatalog.h
@@ -135,6 +135,7 @@ public:
     static DatabaseCatalog & instance();
     static void shutdown();
 
+    void createBackgroundTasks();
     void initializeAndLoadTemporaryDatabase();
     void startupBackgroundCleanup();
     void loadMarkedAsDroppedTables();