diff --git a/edgraph/multi_tenancy_ee.go b/edgraph/multi_tenancy_ee.go
index 0f3bb5759f2..22abeada191 100644
--- a/edgraph/multi_tenancy_ee.go
+++ b/edgraph/multi_tenancy_ee.go
@@ -110,9 +110,6 @@ func (s *Server) CreateNamespace(ctx context.Context, passwd string) (uint64, er
 		return 0, err
 	}
 
-	if err = worker.WaitForIndexing(ctx, true); err != nil {
-		return 0, errors.Wrap(err, "Creating namespace, got error: ")
-	}
 	err = x.RetryUntilSuccess(10, 100*time.Millisecond, func() error {
 		return createGuardianAndGroot(ctx, ids.StartId, passwd)
 	})
diff --git a/worker/draft.go b/worker/draft.go
index fb65e3b545f..a851e2ddb2d 100644
--- a/worker/draft.go
+++ b/worker/draft.go
@@ -195,6 +195,13 @@ func (n *node) waitForTask(id op) {
 	closer.Wait()
 }
 
+func (n *node) isRunningTask(id op) bool {
+	n.opsLock.Lock()
+	_, ok := n.ops[id]
+	n.opsLock.Unlock()
+	return ok
+}
+
 func (n *node) stopAllTasks() {
 	defer n.closer.Done() // CLOSER:1
 	<-n.closer.HasBeenClosed()
diff --git a/worker/mutation.go b/worker/mutation.go
index 584a166920a..ccafab98e6f 100644
--- a/worker/mutation.go
+++ b/worker/mutation.go
@@ -176,13 +176,6 @@ func runSchemaMutation(ctx context.Context, updates []*pb.SchemaUpdate, startTs
 		}
 	}
 
-	// Ensure that rollup is not running.
-	closer, err := gr.Node.startTask(opIndexing)
-	if err != nil {
-		return err
-	}
-	defer stopIndexing(closer)
-
 	buildIndexesHelper := func(update *pb.SchemaUpdate, rebuild posting.IndexRebuild) error {
 		wrtCtx := schema.GetWriteContext(context.Background())
 		if err := rebuild.BuildIndexes(wrtCtx); err != nil {
@@ -214,9 +207,9 @@ func runSchemaMutation(ctx context.Context, updates []*pb.SchemaUpdate, startTs
 	// "Too many open files" error.
 	throttle := y.NewThrottle(maxOpenFileLimit / 8)
 
-	buildIndexes := func(update *pb.SchemaUpdate, rebuild posting.IndexRebuild) {
+	buildIndexes := func(update *pb.SchemaUpdate, rebuild posting.IndexRebuild, c *z.Closer) {
 		// In case background indexing is running, we should call it here again.
-		defer stopIndexing(closer)
+		defer stopIndexing(c)
 
 		// We should only start building indexes once this function has returned.
 		// This is in order to ensure that we do not call DropPrefix for one predicate
@@ -233,6 +226,7 @@ func runSchemaMutation(ctx context.Context, updates []*pb.SchemaUpdate, startTs
 		throttle.Done(nil)
 	}
 
+	var closer *z.Closer
 	for _, su := range updates {
 		if tablet, err := groups().Tablet(su.Predicate); err != nil {
 			return err
@@ -251,6 +245,17 @@ func runSchemaMutation(ctx context.Context, updates []*pb.SchemaUpdate, startTs
 			OldSchema:     &old,
 			CurrentSchema: su,
 		}
+		shouldRebuild := ok && rebuild.NeedIndexRebuild()
+
+		// Start opIndexing task only if schema update needs to build the indexes.
+		if shouldRebuild && !gr.Node.isRunningTask(opIndexing) {
+			closer, err = gr.Node.startTask(opIndexing)
+			if err != nil {
+				return err
+			}
+			defer stopIndexing(closer)
+		}
+
 		querySchema := rebuild.GetQuerySchema()
 		// Sets the schema only in memory. The schema is written to
 		// disk only after schema mutations are successful.
@@ -273,8 +278,8 @@ func runSchemaMutation(ctx context.Context, updates []*pb.SchemaUpdate, startTs
 			return err
 		}
 
-		if ok && rebuild.NeedIndexRebuild() {
-			go buildIndexes(su, rebuild)
+		if shouldRebuild {
+			go buildIndexes(su, rebuild, closer)
 		} else if err := updateSchema(su); err != nil {
 			return err
 		}