diff --git a/db/legacy_schema_tables.cc b/db/legacy_schema_tables.cc
index 3d0b58a4c4..c6ee9220e2 100644
--- a/db/legacy_schema_tables.cc
+++ b/db/legacy_schema_tables.cc
@@ -479,6 +479,16 @@ future<> save_system_keyspace_schema() {
     }
 #endif
 
+    static semaphore the_merge_lock;
+
+    future<> merge_lock() {
+        return smp::submit_to(0, [] { return the_merge_lock.wait(); });
+    }
+
+    future<> merge_unlock() {
+        return smp::submit_to(0, [] { the_merge_lock.signal(); });
+    }
+
     /**
      * Merge remote schema in form of mutations with local and mutate ks/cf metadata objects
      * (which also involves fs operations on add/drop ks/cf)
@@ -490,12 +500,25 @@ future<> save_system_keyspace_schema() {
      */
     future<> merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutations)
     {
-        return merge_schema(proxy, std::move(mutations), true).then([&proxy] {
-            return update_schema_version_and_announce(proxy);
+        return merge_lock().then([&proxy, mutations = std::move(mutations)] {
+            return do_merge_schema(proxy, std::move(mutations), true).then([&proxy] {
+                return update_schema_version_and_announce(proxy);
+            });
+        }).finally([] {
+            return merge_unlock();
         });
     }
 
     future<> merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutations, bool do_flush)
+    { 
+        return merge_lock().then([&proxy, mutations = std::move(mutations), do_flush] {
+            return merge_schema(proxy, std::move(mutations), do_flush);
+        }).finally([] {
+            return merge_unlock();
+        });
+    }
+
+    future<> do_merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutations, bool do_flush)
     {
        return seastar::async([&proxy, mutations = std::move(mutations), do_flush] {
            schema_ptr s = keyspaces();
@@ -532,8 +555,6 @@ future<> save_system_keyspace_schema() {
            /*auto& new_functions = */read_schema_for_keyspaces(proxy, FUNCTIONS, keyspaces).get0();
            /*auto& new_aggregates = */read_schema_for_keyspaces(proxy, AGGREGATES, keyspaces).get0();
 
-           // FIXME: Make the update atomic like in Origin.
-
            std::set<sstring> keyspaces_to_drop = merge_keyspaces(proxy, std::move(old_keyspaces), std::move(new_keyspaces)).get0();
            merge_tables(proxy, std::move(old_column_families), std::move(new_column_families)).get0();
 #if 0
diff --git a/db/legacy_schema_tables.hh b/db/legacy_schema_tables.hh
index 3bd0305e8c..092d64ec43 100644
--- a/db/legacy_schema_tables.hh
+++ b/db/legacy_schema_tables.hh
@@ -65,6 +65,8 @@ future<> merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutat
 
 future<> merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutations, bool do_flush);
 
+future<> do_merge_schema(service::storage_proxy& proxy, std::vector<mutation> mutations, bool do_flush);
+
 future<std::set<sstring>> merge_keyspaces(service::storage_proxy& proxy, schema_result&& before, schema_result&& after);
 
 std::vector<mutation> make_create_keyspace_mutations(lw_shared_ptr<keyspace_metadata> keyspace, api::timestamp_type timestamp, bool with_tables_and_types_and_functions = true);