diff --git a/eng/update-dependencies/SpecificCommand.cs b/eng/update-dependencies/SpecificCommand.cs
index ea9a2043e4..5d1e2f85e6 100644
--- a/eng/update-dependencies/SpecificCommand.cs
+++ b/eng/update-dependencies/SpecificCommand.cs
@@ -274,12 +274,15 @@ await prCreator.CreateOrUpdateAsync(
                 }
                 else
                 {
-                    UpdateExistingGitHubPullRequest(gitHubAuth, prOptions, commitMessage, upstreamBranch);
+                    await UpdateExistingGitHubPullRequestAsync(
+                        client, upstreamProject, pullRequestToUpdate.Number,
+                        gitHubAuth, prOptions, commitMessage, upstreamBranch);
                 }
             }
         }
 
-        private static void UpdateExistingGitHubPullRequest(
+        private static async Task UpdateExistingGitHubPullRequestAsync(
+            GitHubClient client, GitHubProject upstreamProject, int pullRequestNumber,
             GitHubAuth gitHubAuth, PullRequestOptions prOptions, string commitMessage, GitHubBranch upstreamBranch)
         {
             // PullRequestCreator ends up force-pushing updates to an existing PR which is not great when the logic
@@ -308,13 +311,46 @@ private static void UpdateExistingGitHubPullRequest(
                 // Clone the PR's repo/branch to a temp location
                 Repository.Clone($"https://github.com/{gitHubAuth.User}/{Options.GitHubProject}", tempRepoPath, cloneOptions);
 
+                using Repository repo = new(tempRepoPath);
+
+                // Add upstream remote and fetch the target branch so we can find the merge base
+                string upstreamUrl = $"https://github.com/{Options.GitHubUpstreamOwner}/{Options.GitHubProject}";
+                repo.Network.Remotes.Add("upstream", upstreamUrl);
+                Commands.Fetch(repo, "upstream", [$"refs/heads/{upstreamBranch.Name}:refs/remotes/upstream/{upstreamBranch.Name}"], null, null);
+
+                // Check for non-bot commits on the PR branch. If someone other than the bot
+                // has pushed commits, we should not overwrite them.
+                List<string> nonBotCommits = GetNonBotCommits(repo, upstreamBranch.Name);
+                if (nonBotCommits.Count > 0)
+                {
+                    Trace.WriteLine($"Found {nonBotCommits.Count} non-bot commit(s) on the PR branch - skipping update.");
+
+                    string localCommand = BuildLocalUpdateCommand();
+                    string nonBotCommitList = string.Join("\n", nonBotCommits.Select(c => $"- {c}"));
+                    string comment = $"""
+                        Automatic update skipped because additional commits were detected on this branch:
+
+                        {nonBotCommitList}
+
+                        To apply this update manually, run:
+
+                        ```
+                        {localCommand}
+                        ```
+
+                        To allow automatic updates to resume, merge or close this PR.
+                        """;
+
+                    await client.PostCommentAsync(upstreamProject, pullRequestNumber, comment);
+                    return;
+                }
+
                 // Remove all existing directories and files from the temp repo
                 ClearRepoContents(tempRepoPath);
 
                 // Copy contents of local repo changes to temp repo
                 DirectoryCopy(".", tempRepoPath);
 
-                using Repository repo = new(tempRepoPath);
                 RepositoryStatus status = repo.RetrieveStatus(new StatusOptions());
 
                 // If there are any changes from what exists in the PR
@@ -355,6 +391,78 @@ private static void UpdateExistingGitHubPullRequest(
             }
         }
 
+        /// <summary>
+        /// Finds commits on the current branch that were not authored by the bot user.
+        /// Walks the commit log from HEAD back to the merge base with the target branch.
+        /// </summary>
+        private static List<string> GetNonBotCommits(Repository repo, string targetBranchName)
+        {
+            List<string> nonBotCommits = [];
+
+            Branch? targetBranch = repo.Branches[$"upstream/{targetBranchName}"];
+            if (targetBranch is null)
+            {
+                Trace.WriteLine($"Could not find remote tracking branch 'upstream/{targetBranchName}' - skipping non-bot commit check.");
+                return nonBotCommits;
+            }
+
+            Commit headCommit = repo.Head.Tip;
+            Commit targetCommit = targetBranch.Tip;
+
+            Commit? mergeBase = repo.ObjectDatabase.FindMergeBase(headCommit, targetCommit);
+            if (mergeBase is null)
+            {
+                Trace.WriteLine("Could not find merge base - skipping non-bot commit check.");
+                return nonBotCommits;
+            }
+
+            foreach (Commit commit in repo.Commits)
+            {
+                if (commit.Sha == mergeBase.Sha)
+                {
+                    break;
+                }
+
+                if (!string.Equals(commit.Author.Name, Options.User, StringComparison.OrdinalIgnoreCase))
+                {
+                    nonBotCommits.Add($"`{commit.Sha[..7]}` {commit.MessageShort} (by {commit.Author.Name})");
+                }
+            }
+
+            return nonBotCommits;
+        }
+
+        /// <summary>
+        /// Builds a CLI command string that can be run locally to apply the same dependency update.
+        /// Uses the <c>specific</c> subcommand with already-resolved versions, so no BAR auth is needed.
+        /// </summary>
+        private static string BuildLocalUpdateCommand()
+        {
+            List<string> parts =
+            [
+                "dotnet run --project eng/update-dependencies/update-dependencies.csproj --",
+                "specific",
+                Options.DockerfileVersion,
+            ];
+
+            foreach (var (name, version) in Options.ProductVersions)
+            {
+                parts.Add($"--product-version {name}={version}");
+            }
+
+            foreach (string tool in Options.Tools)
+            {
+                parts.Add($"--tool {tool}");
+            }
+
+            if (!string.IsNullOrEmpty(Options.VersionSourceName))
+            {
+                parts.Add($"--version-source-name '{Options.VersionSourceName}'");
+            }
+
+            return string.Join(" ", parts);
+        }
+
         private static void DeleteRepoDirectory(string repoPath)
         {
             if (Directory.Exists(repoPath))