diff --git a/src/mito2/src/engine/staging_test.rs b/src/mito2/src/engine/staging_test.rs
index a883c53106..137a9e9b5f 100644
--- a/src/mito2/src/engine/staging_test.rs
+++ b/src/mito2/src/engine/staging_test.rs
@@ -17,11 +17,12 @@
 use std::fs;
 
 use api::v1::Rows;
+use common_recordbatch::RecordBatches;
 use store_api::region_engine::{RegionEngine, SettableRegionRoleState};
 use store_api::region_request::{
     RegionAlterRequest, RegionFlushRequest, RegionRequest, RegionTruncateRequest,
 };
-use store_api::storage::RegionId;
+use store_api::storage::{RegionId, ScanRequest};
 
 use crate::config::MitoConfig;
 use crate::region::{RegionLeaderState, RegionRoleState};
@@ -329,9 +330,10 @@ async fn test_staging_exit_success_with_manifests() {
         .unwrap()
         .collect::<Result<Vec<_>, _>>()
         .unwrap();
-    assert!(
-        !staging_files_before.is_empty(),
-        "Staging manifest directory should contain files before exit"
+    assert_eq!(
+        staging_files_before.len(),
+        2,
+        "Staging manifest directory should contain two files before exit"
     );
 
     // Count normal manifest files before exit
@@ -341,6 +343,31 @@ async fn test_staging_exit_success_with_manifests() {
         .collect::<Result<Vec<_>, _>>()
         .unwrap();
     let normal_count_before = normal_files_before.len();
+    assert_eq!(
+        normal_count_before, 1,
+        "Normal manifest directory should initially contain one file"
+    );
+
+    // Try read data before exiting staging, SST files should be invisible
+    let request = ScanRequest::default();
+    let scanner = engine.scanner(region_id, request).await.unwrap();
+    assert_eq!(
+        scanner.num_files(),
+        0,
+        "No SST files should be scanned before exit"
+    );
+    assert_eq!(
+        scanner.num_memtables(),
+        0,
+        "Memtables should be removed in staging before exit"
+    );
+    let stream = scanner.scan().await.unwrap();
+    let batches = RecordBatches::try_collect(stream).await.unwrap();
+    let total_rows: usize = batches.iter().map(|rb| rb.num_rows()).sum();
+    assert_eq!(
+        total_rows, 0,
+        "No data should be readable before exit staging mode"
+    );
 
     // Exit staging mode successfully
     engine
@@ -374,4 +401,27 @@ async fn test_staging_exit_success_with_manifests() {
         normal_files_after.len() > normal_count_before,
         "Normal manifest directory should contain more files after merge"
     );
+
+    // Validate in-memory version reflects merged manifests (files visible in levels)
+    let version = region.version();
+    let levels = version.ssts.levels();
+    assert!(
+        !levels.is_empty() && !levels[0].files.is_empty(),
+        "SST levels should have files after exiting staging"
+    );
+
+    // Also ensure scanner behavior reflects 2 SSTs
+    let request = ScanRequest::default();
+    let scanner = engine.scanner(region_id, request).await.unwrap();
+    assert_eq!(
+        scanner.num_files(),
+        2,
+        "SST files should be scanned after exit"
+    );
+
+    // Try reading data via scanner to ensure previous staged data is actually readable
+    let stream = scanner.scan().await.unwrap();
+    let batches = RecordBatches::try_collect(stream).await.unwrap();
+    let total_rows: usize = batches.iter().map(|rb| rb.num_rows()).sum();
+    assert_eq!(total_rows, 10, "Expected to read all staged rows");
 }
diff --git a/src/mito2/src/flush.rs b/src/mito2/src/flush.rs
index 0c8e40dda5..cc40b6fed0 100644
--- a/src/mito2/src/flush.rs
+++ b/src/mito2/src/flush.rs
@@ -1012,14 +1012,14 @@ mod tests {
             .collect();
         // Assumes the flush job is finished.
         version_control.apply_edit(
-            RegionEdit {
+            Some(RegionEdit {
                 files_to_add: Vec::new(),
                 files_to_remove: Vec::new(),
                 timestamp_ms: None,
                 compaction_time_window: None,
                 flushed_entry_id: None,
                 flushed_sequence: None,
-            },
+            }),
             &[0],
             builder.file_purger(),
         );
diff --git a/src/mito2/src/manifest/action.rs b/src/mito2/src/manifest/action.rs
index c4de57896c..85b8677b0a 100644
--- a/src/mito2/src/manifest/action.rs
+++ b/src/mito2/src/manifest/action.rs
@@ -368,6 +368,38 @@ impl RegionMetaActionList {
     pub fn new(actions: Vec<RegionMetaAction>) -> Self {
         Self { actions }
     }
+
+    pub fn into_region_edit(self) -> RegionEdit {
+        let mut edit = RegionEdit {
+            files_to_add: Vec::new(),
+            files_to_remove: Vec::new(),
+            timestamp_ms: None,
+            compaction_time_window: None,
+            flushed_entry_id: None,
+            flushed_sequence: None,
+        };
+
+        for action in self.actions {
+            if let RegionMetaAction::Edit(region_edit) = action {
+                // Merge file adds/removes
+                edit.files_to_add.extend(region_edit.files_to_add);
+                edit.files_to_remove.extend(region_edit.files_to_remove);
+                // Max of flushed entry id / sequence
+                if let Some(eid) = region_edit.flushed_entry_id {
+                    edit.flushed_entry_id = Some(edit.flushed_entry_id.map_or(eid, |v| v.max(eid)));
+                }
+                if let Some(seq) = region_edit.flushed_sequence {
+                    edit.flushed_sequence = Some(edit.flushed_sequence.map_or(seq, |v| v.max(seq)));
+                }
+                // Prefer the latest non-none time window
+                if region_edit.compaction_time_window.is_some() {
+                    edit.compaction_time_window = region_edit.compaction_time_window;
+                }
+            }
+        }
+
+        edit
+    }
 }
 
 impl RegionMetaActionList {
diff --git a/src/mito2/src/region.rs b/src/mito2/src/region.rs
index b657b107ec..e280ebe493 100644
--- a/src/mito2/src/region.rs
+++ b/src/mito2/src/region.rs
@@ -621,13 +621,18 @@ impl MitoRegion {
         // Submit merged actions using the manifest manager's update method
         // Pass the target state (Writable) so it saves to normal directory, not staging
         let target_state = RegionRoleState::Leader(RegionLeaderState::Writable);
-        let new_version = manager.update(merged_actions, target_state).await?;
+        let new_version = manager.update(merged_actions.clone(), target_state).await?;
 
         info!(
             "Successfully submitted merged staged manifests for region {}, new version: {}",
             self.region_id, new_version
         );
 
+        // Apply the merged changes to in-memory version control
+        let merged_edit = merged_actions.into_region_edit();
+        self.version_control
+            .apply_edit(Some(merged_edit), &[], self.file_purger.clone());
+
         // Clear all staging manifests and transit state
         manager.store().clear_staging_manifests().await?;
         self.exit_staging()?;
@@ -782,7 +787,7 @@ impl ManifestContext {
 
     /// Sets the [`RegionRole`].
     ///
-    /// ```
+    /// ```text
     ///     +------------------------------------------+
     ///     |                      +-----------------+ |
     ///     |                      |                 | |
diff --git a/src/mito2/src/region/version.rs b/src/mito2/src/region/version.rs
index 6a62219855..e37ed743ce 100644
--- a/src/mito2/src/region/version.rs
+++ b/src/mito2/src/region/version.rs
@@ -127,19 +127,22 @@ impl VersionControl {
     }
 
     /// Apply edit to current version.
+    ///
+    /// If `edit` is None, only removes the specified memtables.
     pub(crate) fn apply_edit(
         &self,
-        edit: RegionEdit,
+        edit: Option<RegionEdit>,
         memtables_to_remove: &[MemtableId],
         purger: FilePurgerRef,
     ) {
         let version = self.current().version;
-        let new_version = Arc::new(
-            VersionBuilder::from_version(version)
-                .apply_edit(edit, purger)
-                .remove_memtables(memtables_to_remove)
-                .build(),
-        );
+        let builder = VersionBuilder::from_version(version);
+        let builder = if let Some(edit) = edit {
+            builder.apply_edit(edit, purger)
+        } else {
+            builder
+        };
+        let new_version = Arc::new(builder.remove_memtables(memtables_to_remove).build());
 
         let mut version_data = self.data.write().unwrap();
         version_data.version = new_version;
diff --git a/src/mito2/src/test_util/version_util.rs b/src/mito2/src/test_util/version_util.rs
index d023e50f53..16fe0eaa12 100644
--- a/src/mito2/src/test_util/version_util.rs
+++ b/src/mito2/src/test_util/version_util.rs
@@ -204,14 +204,14 @@ pub(crate) fn apply_edit(
         .collect();
 
     version_control.apply_edit(
-        RegionEdit {
+        Some(RegionEdit {
             files_to_add,
             files_to_remove: files_to_remove.to_vec(),
             timestamp_ms: None,
             compaction_time_window: None,
             flushed_entry_id: None,
             flushed_sequence: None,
-        },
+        }),
         &[],
         purger,
     );
diff --git a/src/mito2/src/worker/handle_compaction.rs b/src/mito2/src/worker/handle_compaction.rs
index b74819a733..b9aa7baa38 100644
--- a/src/mito2/src/worker/handle_compaction.rs
+++ b/src/mito2/src/worker/handle_compaction.rs
@@ -74,9 +74,11 @@ impl<S> RegionWorkerLoop<S> {
         };
         region.update_compaction_millis();
 
-        region
-            .version_control
-            .apply_edit(request.edit.clone(), &[], region.file_purger.clone());
+        region.version_control.apply_edit(
+            Some(request.edit.clone()),
+            &[],
+            region.file_purger.clone(),
+        );
 
         // compaction finished.
         request.on_success();
diff --git a/src/mito2/src/worker/handle_flush.rs b/src/mito2/src/worker/handle_flush.rs
index aabee2db4f..336d198ce5 100644
--- a/src/mito2/src/worker/handle_flush.rs
+++ b/src/mito2/src/worker/handle_flush.rs
@@ -215,9 +215,14 @@ impl<S: LogStore> RegionWorkerLoop<S> {
                 "Skipping region metadata update for region {} in staging mode",
                 region_id
             );
+            region.version_control.apply_edit(
+                None,
+                &request.memtables_to_remove,
+                region.file_purger.clone(),
+            );
         } else {
             region.version_control.apply_edit(
-                request.edit.clone(),
+                Some(request.edit.clone()),
                 &request.memtables_to_remove,
                 region.file_purger.clone(),
             );
diff --git a/src/mito2/src/worker/handle_manifest.rs b/src/mito2/src/worker/handle_manifest.rs
index 6e897be971..4fb32befed 100644
--- a/src/mito2/src/worker/handle_manifest.rs
+++ b/src/mito2/src/worker/handle_manifest.rs
@@ -262,9 +262,11 @@ impl<S> RegionWorkerLoop<S> {
 
         if edit_result.result.is_ok() {
             // Applies the edit to the region.
-            region
-                .version_control
-                .apply_edit(edit_result.edit, &[], region.file_purger.clone());
+            region.version_control.apply_edit(
+                Some(edit_result.edit),
+                &[],
+                region.file_purger.clone(),
+            );
         }
 
         // Sets the region as writable.