diff --git a/src/storage/src/manifest/region.rs b/src/storage/src/manifest/region.rs
index 204cc8abf07f..fa1b9de06ad8 100644
--- a/src/storage/src/manifest/region.rs
+++ b/src/storage/src/manifest/region.rs
@@ -44,8 +44,10 @@ pub struct RegionManifestCheckpointer {
 
 impl RegionManifestCheckpointer {
     pub(crate) fn set_flushed_manifest_version(&self, manifest_version: ManifestVersion) {
+        let current = self.flushed_manifest_version.load(Ordering::Relaxed);
+
         self.flushed_manifest_version
-            .store(manifest_version, Ordering::Relaxed);
+            .store(current.max(manifest_version), Ordering::Relaxed);
     }
 }
 
diff --git a/src/storage/src/region.rs b/src/storage/src/region.rs
index c177ffb78563..9deda381c634 100644
--- a/src/storage/src/region.rs
+++ b/src/storage/src/region.rs
@@ -356,6 +356,11 @@ impl<S: LogStore> RegionImpl<S> {
             .replay(recovered_metadata_after_flushed, writer_ctx)
             .await?;
 
+        // Update flushed manifest version after replaying
+        store_config
+            .manifest
+            .set_flushed_manifest_version(shared.version_control.current().manifest_version());
+
         let inner = Arc::new(RegionInner {
             shared,
             writer,