diff --git a/src/Storages/StorageMergeTree.cpp b/src/Storages/StorageMergeTree.cpp
index a46b85364be0..1cc616bd8521 100644
--- a/src/Storages/StorageMergeTree.cpp
+++ b/src/Storages/StorageMergeTree.cpp
@@ -256,6 +256,11 @@ void StorageMergeTree::shutdown(bool)
 
     if (deduplication_log)
         deduplication_log->shutdown();
+
+    {
+        std::lock_guard lock(export_manifests_mutex);
+        export_manifests.clear();
+    }
 }
 
 
diff --git a/src/Storages/StorageReplicatedMergeTree.cpp b/src/Storages/StorageReplicatedMergeTree.cpp
index 0b7c3c600e5f..ec6c43ff775e 100644
--- a/src/Storages/StorageReplicatedMergeTree.cpp
+++ b/src/Storages/StorageReplicatedMergeTree.cpp
@@ -6014,6 +6014,17 @@ void StorageReplicatedMergeTree::shutdown(bool)
         /// Wait for all of them
         std::lock_guard lock(data_parts_exchange_ptr->rwlock);
     }
+
+    {
+        std::lock_guard lock(export_merge_tree_partition_mutex);
+        export_merge_tree_partition_task_entries.clear();
+    }
+
+    {
+        std::lock_guard lock(export_manifests_mutex);
+        export_manifests.clear();
+    }
+
     LOG_TRACE(log, "Shutdown finished");
 }