diff --git a/src-tauri/src/auto_updater.rs b/src-tauri/src/auto_updater.rs
index 60a35ac..4924a84 100644
--- a/src-tauri/src/auto_updater.rs
+++ b/src-tauri/src/auto_updater.rs
@@ -458,6 +458,39 @@ impl AutoUpdater {
 
     Ok(())
   }
+
+  /// Get pending update versions for a specific browser
+  /// Returns a set of (browser, version) pairs that have pending updates
+  pub fn get_pending_update_versions(
+    &self,
+  ) -> Result<std::collections::HashSet<(String, String)>, Box<dyn std::error::Error + Send + Sync>>
+  {
+    let state = self.load_auto_update_state()?;
+    let mut pending_versions = std::collections::HashSet::new();
+
+    for update in &state.pending_updates {
+      pending_versions.insert((update.browser.clone(), update.new_version.clone()));
+    }
+
+    Ok(pending_versions)
+  }
+
+  /// Get pending update for a specific browser version if it exists
+  pub fn get_pending_update(
+    &self,
+    browser: &str,
+    current_version: &str,
+  ) -> Result<Option<UpdateNotification>, Box<dyn std::error::Error + Send + Sync>> {
+    let state = self.load_auto_update_state()?;
+
+    for update in &state.pending_updates {
+      if update.browser == browser && update.current_version == current_version {
+        return Ok(Some(update.clone()));
+      }
+    }
+
+    Ok(None)
+  }
 }
 
 // Tauri commands
diff --git a/src-tauri/src/browser_runner.rs b/src-tauri/src/browser_runner.rs
index 9cd3de7..5e80397 100644
--- a/src-tauri/src/browser_runner.rs
+++ b/src-tauri/src/browser_runner.rs
@@ -1007,6 +1007,19 @@ impl BrowserRunner {
     })
   }
 
+  /// Update a profile's browser version
+  pub fn update_profile_version(
+    &self,
+    app_handle: &tauri::AppHandle,
+    profile_id: &str,
+    version: &str,
+  ) -> Result<BrowserProfile, Box<dyn std::error::Error + Send + Sync>> {
+    let profile_manager = ProfileManager::instance();
+    profile_manager
+      .update_profile_version(app_handle, profile_id, version)
+      .map_err(|e| format!("Failed to update profile version: {e}").into())
+  }
+
   pub fn delete_profile(
     &self,
     app_handle: tauri::AppHandle,
@@ -1110,6 +1123,45 @@ impl BrowserRunner {
       // Clear the process ID from the profile
       let mut updated_profile = profile.clone();
       updated_profile.process_id = None;
+
+      // Check for pending updates and apply them for Camoufox profiles too
+      let auto_updater = crate::auto_updater::AutoUpdater::instance();
+      if let Ok(Some(pending_update)) =
+        auto_updater.get_pending_update(&profile.browser, &profile.version)
+      {
+        println!(
+          "Found pending update for Camoufox profile {}: {} -> {}",
+          profile.name, profile.version, pending_update.new_version
+        );
+
+        // Update the profile to the new version
+        match self.update_profile_version(
+          &app_handle,
+          &profile.id.to_string(),
+          &pending_update.new_version,
+        ) {
+          Ok(updated_profile_after_update) => {
+            println!(
+              "Successfully updated Camoufox profile {} from version {} to {}",
+              profile.name, profile.version, pending_update.new_version
+            );
+            updated_profile = updated_profile_after_update;
+
+            // Remove the pending update from the auto updater state
+            if let Err(e) = auto_updater.dismiss_update_notification(&pending_update.id) {
+              eprintln!("Warning: Failed to dismiss pending update notification: {e}");
+            }
+          }
+          Err(e) => {
+            eprintln!(
+              "Failed to apply pending update for Camoufox profile {}: {}",
+              profile.name, e
+            );
+            // Continue with the original profile update (just clearing process_id)
+          }
+        }
+      }
+
       self
         .save_process_info(&updated_profile)
         .map_err(|e| format!("Failed to update profile: {e}"))?;
@@ -1288,6 +1340,45 @@ impl BrowserRunner {
     // Clear the process ID from the profile
     let mut updated_profile = profile.clone();
     updated_profile.process_id = None;
+
+    // Check for pending updates and apply them
+    let auto_updater = crate::auto_updater::AutoUpdater::instance();
+    if let Ok(Some(pending_update)) =
+      auto_updater.get_pending_update(&profile.browser, &profile.version)
+    {
+      println!(
+        "Found pending update for profile {}: {} -> {}",
+        profile.name, profile.version, pending_update.new_version
+      );
+
+      // Update the profile to the new version
+      match self.update_profile_version(
+        &app_handle,
+        &profile.id.to_string(),
+        &pending_update.new_version,
+      ) {
+        Ok(updated_profile_after_update) => {
+          println!(
+            "Successfully updated profile {} from version {} to {}",
+            profile.name, profile.version, pending_update.new_version
+          );
+          updated_profile = updated_profile_after_update;
+
+          // Remove the pending update from the auto updater state
+          if let Err(e) = auto_updater.dismiss_update_notification(&pending_update.id) {
+            eprintln!("Warning: Failed to dismiss pending update notification: {e}");
+          }
+        }
+        Err(e) => {
+          eprintln!(
+            "Failed to apply pending update for profile {}: {}",
+            profile.name, e
+          );
+          // Continue with the original profile update (just clearing process_id)
+        }
+      }
+    }
+
     self
       .save_process_info(&updated_profile)
       .map_err(|e| format!("Failed to update profile: {e}"))?;
diff --git a/src-tauri/src/downloaded_browsers.rs b/src-tauri/src/downloaded_browsers.rs
index 1a84d3d..74ed6f3 100644
--- a/src-tauri/src/downloaded_browsers.rs
+++ b/src-tauri/src/downloaded_browsers.rs
@@ -202,6 +202,16 @@ impl DownloadedBrowsersRegistry {
       running_profiles.iter().cloned().collect();
     let mut cleaned_up = Vec::new();
 
+    // Get pending update versions from auto updater
+    let pending_updates =
+      match crate::auto_updater::AutoUpdater::instance().get_pending_update_versions() {
+        Ok(updates) => updates,
+        Err(e) => {
+          eprintln!("Warning: Failed to get pending updates for cleanup: {e}");
+          std::collections::HashSet::new()
+        }
+      };
+
     // Collect all downloaded browsers that are not in active profiles
     let mut to_remove = Vec::new();
     {
@@ -222,6 +232,18 @@ impl DownloadedBrowsersRegistry {
             continue;
           }
 
+          // Don't remove if this version has a pending update for a running profile
+          // This handles the case where a running profile has an update downloaded but not yet applied
+          if pending_updates.contains(&browser_version) {
+            // Check if there are any running profiles for this browser that could be updated
+            let has_running_profile_for_browser =
+              running_profiles.iter().any(|(b, _)| b == browser);
+            if has_running_profile_for_browser {
+              println!("Keeping: {browser} {version} (pending update for running profile)");
+              continue;
+            }
+          }
+
           // Mark for removal
           to_remove.push(browser_version);
           println!("Marking for removal: {browser} {version} (not used by any profile)");