diff --git a/tsdb/store.go b/tsdb/store.go
index a22ec8f15a7..bd402ece409 100644
--- a/tsdb/store.go
+++ b/tsdb/store.go
@@ -714,19 +714,20 @@ func (s *Store) DeleteShard(shardID uint64) error {
 		return nil
 	}
 	delete(s.shards, shardID)
-	delete(s.epochs, shardID)
 	s.pendingShardDeletes[shardID] = struct{}{}
 
 	db := sh.Database()
 	// Determine if the shard contained any series that are not present in any
 	// other shards in the database.
 	shards := s.filterShards(byDatabase(db))
+	epoch := s.epochs[shardID]
 	s.mu.Unlock()
 
 	// Ensure the pending deletion flag is cleared on exit.
 	defer func() {
 		s.mu.Lock()
 		defer s.mu.Unlock()
+		delete(s.epochs, shardID)
 		delete(s.pendingShardDeletes, shardID)
 		s.databases[db].removeIndexType(sh.IndexType())
 	}()
@@ -787,6 +788,15 @@ func (s *Store) DeleteShard(shardID uint64) error {
 
 	}
 
+	// enter the epoch tracker
+	guards, gen := epoch.StartWrite()
+	defer epoch.EndWrite(gen)
+
+	// wait for any guards before closing the shard
+	for _, guard := range guards {
+		guard.Wait()
+	}
+
 	// Close the shard.
 	if err := sh.Close(); err != nil {
 		return err
@@ -808,9 +818,8 @@ func (s *Store) DeleteDatabase(name string) error {
 		// no files locally, so nothing to do
 		return nil
 	}
-	shards := s.filterShards(func(sh *Shard) bool {
-		return sh.database == name
-	})
+	shards := s.filterShards(byDatabase(name))
+	epochs := s.epochsForShards(shards)
 	s.mu.RUnlock()
 
 	if err := s.walkShards(shards, func(sh *Shard) error {
@@ -818,6 +827,16 @@ func (s *Store) DeleteDatabase(name string) error {
 			return nil
 		}
 
+		epoch := epochs[sh.id]
+		// enter the epoch tracker
+		guards, gen := epoch.StartWrite()
+		defer epoch.EndWrite(gen)
+
+		// wait for any guards before closing the shard
+		for _, guard := range guards {
+			guard.Wait()
+		}
+
 		return sh.Close()
 	}); err != nil {
 		return err