diff --git a/etcdserver/api/snap/snapshotter.go b/etcdserver/api/snap/snapshotter.go
index 7e7933374c9..409aed386b6 100644
--- a/etcdserver/api/snap/snapshotter.go
+++ b/etcdserver/api/snap/snapshotter.go
@@ -226,6 +226,9 @@ func (s *Snapshotter) snapNames() ([]string, error) {
 	if err != nil {
 		return nil, err
 	}
+	if err = s.cleanupSnapdir(names); err != nil {
+		return nil, err
+	}
 	snaps := checkSuffix(s.lg, names)
 	if len(snaps) == 0 {
 		return nil, ErrNoSnapshot
@@ -253,3 +256,21 @@ func checkSuffix(lg *zap.Logger, names []string) []string {
 	}
 	return snaps
 }
+
+// cleanupSnapdir removes any files that should not be in the snapshot directory:
+// - db.tmp prefixed files that can be orphaned by defragmentation
+func (s *Snapshotter) cleanupSnapdir(filenames []string) error {
+	for _, filename := range filenames {
+		if strings.HasPrefix(filename, "db.tmp") {
+			if s.lg != nil {
+				s.lg.Info("found orphaned defragmentation file; deleting", zap.String("path", filename))
+			} else {
+				plog.Infof("found orphaned defragmentation file; deleting: %s", filename)
+			}
+			if rmErr := os.Remove(filepath.Join(s.dir, filename)); rmErr != nil && !os.IsNotExist(rmErr) {
+				return fmt.Errorf("failed to remove orphaned defragmentation file %s: %v", filename, rmErr)
+			}
+		}
+	}
+	return nil
+}
diff --git a/mvcc/backend/backend.go b/mvcc/backend/backend.go
index bffd74950b4..6cbf3e66709 100644
--- a/mvcc/backend/backend.go
+++ b/mvcc/backend/backend.go
@@ -369,13 +369,24 @@ func (b *backend) defrag() error {
 
 	b.batchTx.tx = nil
 
-	tmpdb, err := bolt.Open(b.db.Path()+".tmp", 0600, boltOpenOptions)
+	// Create a temporary file to ensure we start with a clean slate.
+	// Snapshotter.cleanupSnapdir cleans up any of these that are found during startup.
+	dir := filepath.Dir(b.db.Path())
+	temp, err := ioutil.TempFile(dir, "db.tmp.*")
+	if err != nil {
+		return err
+	}
+	options := *boltOpenOptions
+	options.OpenFile = func(path string, i int, mode os.FileMode) (file *os.File, err error) {
+		return temp, nil
+	}
+	tdbp := temp.Name()
+	tmpdb, err := bolt.Open(tdbp, 0600, &options)
 	if err != nil {
 		return err
 	}
 
 	dbp := b.db.Path()
-	tdbp := tmpdb.Path()
 	size1, sizeInUse1 := b.Size(), b.SizeInUse()
 	if b.lg != nil {
 		b.lg.Info(
@@ -387,11 +398,17 @@ func (b *backend) defrag() error {
 			zap.String("current-db-size-in-use", humanize.Bytes(uint64(sizeInUse1))),
 		)
 	}
-
+	// gofail: var defragBeforeCopy struct{}
 	err = defragdb(b.db, tmpdb, defragLimit)
 	if err != nil {
 		tmpdb.Close()
-		os.RemoveAll(tmpdb.Path())
+		if rmErr := os.RemoveAll(tmpdb.Path()); rmErr != nil {
+			if b.lg != nil {
+				b.lg.Error("failed to remove db.tmp after defragmentation completed", zap.Error(rmErr))
+			} else {
+				plog.Fatalf("failed to remove db.tmp after defragmentation completed: %v", rmErr)
+			}
+		}
 		return err
 	}
 
@@ -411,6 +428,7 @@ func (b *backend) defrag() error {
 			plog.Fatalf("cannot close database (%s)", err)
 		}
 	}
+	// gofail: var defragBeforeRename struct{}
 	err = os.Rename(tdbp, dbp)
 	if err != nil {
 		if b.lg != nil {