diff --git a/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/BookmarkManagerTests.cs b/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/BookmarkManagerTests.cs
index 0751b5afe3..b4e533d66d 100644
--- a/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/BookmarkManagerTests.cs
+++ b/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/BookmarkManagerTests.cs
@@ -186,4 +186,48 @@ public class BookmarkManagerTests
         Assert.AreEqual("D:\\UpdatedPath", updatedBookmark.Bookmark);
         Assert.IsTrue(bookmarkUpdatedEventFired);
     }
+
+    [TestMethod]
+    public void BookmarkManager_LegacyData_IdsArePersistedAcrossLoads()
+    {
+        // Arrange
+        const string json = """
+                            {
+                                "Data": 
+                                [
+                                    { "Name": "C:\\","Bookmark": "C:\\" },
+                                    { "Name": "Bing.com","Bookmark": "https://bing.com" }
+                                ]
+                            }
+                            """;
+
+        var dataSource = new MockBookmarkDataSource(json);
+
+        // First load: IDs should be generated for legacy entries
+        var manager1 = new BookmarksManager(dataSource);
+        var firstLoad = manager1.Bookmarks.ToList();
+        Assert.AreEqual(2, firstLoad.Count);
+        Assert.AreNotEqual(Guid.Empty, firstLoad[0].Id);
+        Assert.AreNotEqual(Guid.Empty, firstLoad[1].Id);
+
+        // Keep a name->id map to be insensitive to ordering
+        var firstIdsByName = firstLoad.ToDictionary(b => b.Name, b => b.Id);
+
+        // Wait deterministically for async persistence to complete
+        var wasSaved = dataSource.WaitForSave(1, 5000);
+        Assert.IsTrue(wasSaved, "Data was not saved within the expected time.");
+
+        // Second load: should read back the same IDs from persisted data
+        var manager2 = new BookmarksManager(dataSource);
+        var secondLoad = manager2.Bookmarks.ToList();
+        Assert.AreEqual(2, secondLoad.Count);
+
+        var secondIdsByName = secondLoad.ToDictionary(b => b.Name, b => b.Id);
+
+        foreach (var kvp in firstIdsByName)
+        {
+            Assert.IsTrue(secondIdsByName.ContainsKey(kvp.Key), $"Missing bookmark '{kvp.Key}' after reload.");
+            Assert.AreEqual(kvp.Value, secondIdsByName[kvp.Key], $"Bookmark '{kvp.Key}' upgraded ID was not persisted across loads.");
+        }
+    }
 }
diff --git a/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/MockBookmarkDataSource.cs b/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/MockBookmarkDataSource.cs
index 3980ac13c6..02d71d6d77 100644
--- a/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/MockBookmarkDataSource.cs
+++ b/src/modules/cmdpal/Tests/Microsoft.CmdPal.Ext.Bookmarks.UnitTests/MockBookmarkDataSource.cs
@@ -2,6 +2,8 @@
 // The Microsoft Corporation licenses this file to you under the MIT license.
 // See the LICENSE file in the project root for more information.
 
+using System;
+using System.Threading;
 using Microsoft.CmdPal.Ext.Bookmarks.Persistence;
 
 namespace Microsoft.CmdPal.Ext.Bookmarks.UnitTests;
@@ -9,6 +11,7 @@ namespace Microsoft.CmdPal.Ext.Bookmarks.UnitTests;
 internal sealed class MockBookmarkDataSource : IBookmarkDataSource
 {
     private string _jsonData;
+    private int _saveCount;
 
     public MockBookmarkDataSource(string initialJsonData = "[]")
     {
@@ -23,5 +26,26 @@ internal sealed class MockBookmarkDataSource : IBookmarkDataSource
     public void SaveBookmarkData(string jsonData)
     {
         _jsonData = jsonData;
+        Interlocked.Increment(ref _saveCount);
+    }
+
+    public int SaveCount => Volatile.Read(ref _saveCount);
+
+    // Waits until at least expectedMinSaves have occurred or the timeout elapses.
+    // Returns true if the condition was met, false on timeout.
+    public bool WaitForSave(int expectedMinSaves = 1, int timeoutMs = 2000)
+    {
+        var start = Environment.TickCount;
+        while (Volatile.Read(ref _saveCount) < expectedMinSaves)
+        {
+            if (Environment.TickCount - start > timeoutMs)
+            {
+                return false;
+            }
+
+            Thread.Sleep(50);
+        }
+
+        return true;
     }
 }
diff --git a/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/BookmarksManager.cs b/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/BookmarksManager.cs
index 1eb57fb7eb..fde574360f 100644
--- a/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/BookmarksManager.cs
+++ b/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/BookmarksManager.cs
@@ -103,7 +103,33 @@ internal sealed partial class BookmarksManager : IDisposable, IBookmarksManager
         try
         {
             var jsonData = _dataSource.GetBookmarkData();
-            _bookmarksData = _parser.ParseBookmarks(jsonData);
+            var bookmarksData = _parser.ParseBookmarks(jsonData);
+
+            // Upgrade old bookmarks if necessary
+            // Pre .95 versions did not assign IDs to bookmarks
+            var upgraded = false;
+            for (var index = 0; index < bookmarksData.Data.Count; index++)
+            {
+                var bookmark = bookmarksData.Data[index];
+                if (bookmark.Id == Guid.Empty)
+                {
+                    bookmarksData.Data[index] = bookmark with { Id = Guid.NewGuid() };
+                    upgraded = true;
+                }
+            }
+
+            lock (_lock)
+            {
+                _bookmarksData = bookmarksData;
+            }
+
+            // LOAD BEARING: Save upgraded data back to file
+            // This ensures that old bookmarks are not repeatedly upgraded on each load,
+            // as the hotkeys and aliases are tied to the generated bookmark IDs.
+            if (upgraded)
+            {
+                _ = SaveChangesAsync();
+            }
         }
         catch (Exception ex)
         {
diff --git a/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/Persistence/BookmarkData.cs b/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/Persistence/BookmarkData.cs
index 3129e1b578..b577f9cb35 100644
--- a/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/Persistence/BookmarkData.cs
+++ b/src/modules/cmdpal/ext/Microsoft.CmdPal.Ext.Bookmark/Persistence/BookmarkData.cs
@@ -19,7 +19,7 @@ public sealed record BookmarkData
     [SetsRequiredMembers]
     public BookmarkData(Guid id, string? name, string? bookmark)
     {
-        Id = id == Guid.Empty ? Guid.NewGuid() : id;
+        Id = id;
         Name = name ?? string.Empty;
         Bookmark = bookmark ?? string.Empty;
     }