diff --git a/server/filestore.go b/server/filestore.go
index 58b8ca2aaa..2c37c43f83 100644
--- a/server/filestore.go
+++ b/server/filestore.go
@@ -315,6 +315,11 @@ func newFileStoreWithCreated(fcfg FileStoreConfig, cfg StreamConfig, created tim
 	// Always track per subject information.
 	fs.tms = true
 
+	// Recover our message state.
+	if err := fs.recoverMsgs(); err != nil {
+		return nil, err
+	}
+
 	// Write our meta data iff does not exist.
 	meta := path.Join(fcfg.StoreDir, JetStreamMetaFile)
 	if _, err := os.Stat(meta); err != nil && os.IsNotExist(err) {
@@ -323,11 +328,6 @@ func newFileStoreWithCreated(fcfg FileStoreConfig, cfg StreamConfig, created tim
 		}
 	}
 
-	// Recover our message state.
-	if err := fs.recoverMsgs(); err != nil {
-		return nil, err
-	}
-
 	// If we expect to be encrypted check that what we are restoring is not plaintext.
 	// This can happen on snapshot restores or conversions.
 	if fs.prf != nil {
@@ -4426,6 +4426,13 @@ func (mb *msgBlock) generatePerSubjectInfo() error {
 	for seq := fseq; seq <= lseq; seq++ {
 		sm, err := mb.cacheLookup(seq)
 		if err != nil {
+			// Since we are walking by sequence we can ignore some errors that are benign to rebuilding our state.
+			if err == ErrStoreMsgNotFound || err == errDeletedMsg {
+				continue
+			}
+			if err == errNoCache {
+				return nil
+			}
 			return err
 		}
 		if sm != nil && len(sm.subj) > 0 {
diff --git a/server/jetstream_test.go b/server/jetstream_test.go
index 96b03da85b..c22cce1005 100644
--- a/server/jetstream_test.go
+++ b/server/jetstream_test.go
@@ -15209,6 +15209,51 @@ func TestJetStreamPullConsumerHeartBeats(t *testing.T) {
 	}
 }
 
+func TestJetStreamRecoverStreamWithDeletedMessagesNonCleanShutdown(t *testing.T) {
+	s := RunBasicJetStreamServer()
+	defer s.Shutdown()
+
+	if config := s.JetStreamConfig(); config != nil {
+		defer removeDir(t, config.StoreDir)
+	}
+
+	nc, js := jsClientConnect(t, s)
+	defer nc.Close()
+
+	_, err := js.AddStream(&nats.StreamConfig{Name: "T"})
+	require_NoError(t, err)
+
+	for i := 0; i < 100; i++ {
+		js.Publish("T", []byte("OK"))
+	}
+
+	js.DeleteMsg("T", 22)
+
+	// Now we need a non-clean shutdown.
+	// For this use case that means we do *not* write the fss file.
+	sd := s.JetStreamConfig().StoreDir
+	fss := path.Join(sd, "$G", "streams", "T", "msgs", "1.fss")
+
+	// Stop current
+	nc.Close()
+	s.Shutdown()
+
+	// Remove fss file to simulate a non-clean shutdown.
+	err = os.Remove(fss)
+	require_NoError(t, err)
+
+	// Restart.
+	s = RunJetStreamServerOnPort(-1, sd)
+	defer s.Shutdown()
+
+	nc, js = jsClientConnect(t, s)
+	defer nc.Close()
+
+	// Make sure we recovered our stream
+	_, err = js.StreamInfo("T")
+	require_NoError(t, err)
+}
+
 ///////////////////////////////////////////////////////////////////////////
 // Simple JetStream Benchmarks
 ///////////////////////////////////////////////////////////////////////////