diff --git a/src/Elastic.Codex/Sourcing/CodexCloneService.cs b/src/Elastic.Codex/Sourcing/CodexCloneService.cs
index e0cfd0eca7..a00b906f2d 100644
--- a/src/Elastic.Codex/Sourcing/CodexCloneService.cs
+++ b/src/Elastic.Codex/Sourcing/CodexCloneService.cs
@@ -84,6 +84,11 @@ public class CodexCloneService(ILoggerFactory logFactory, ILinkIndexReader linkI
 			try
 			{
 				var git = new CodexGitRepository(loggerFactory, context.Collector, subDir);
+				if (!git.HasHead())
+				{
+					logger.LogWarning("Could not read commit for {Name}; skipping", repoName);
+					continue;
+				}
 				currentCommit = git.GetCurrentCommit();
 			}
 			catch (OperationCanceledException)
@@ -186,7 +191,10 @@ bool assumeCloned
 
 		try
 		{
-			var git = new CodexGitRepository(logFactory, context.Collector, repoDir);
+			// Git command failures emit collector errors. Use a local collector so a
+			// missing clone token policy warns and skips instead of failing the job.
+			var gitCollector = new DiagnosticsCollector([]);
+			var git = new CodexGitRepository(logFactory, gitCollector, repoDir);
 
 			if (assumeCloned && git.IsInitialized())
 			{
diff --git a/src/Elastic.Codex/Sourcing/CodexGitRepository.cs b/src/Elastic.Codex/Sourcing/CodexGitRepository.cs
index d4ee79e0dc..7457f514c9 100644
--- a/src/Elastic.Codex/Sourcing/CodexGitRepository.cs
+++ b/src/Elastic.Codex/Sourcing/CodexGitRepository.cs
@@ -53,25 +53,34 @@ protected override void OnBeforeRetry() =>
 
 	public bool IsInitialized() => Directory.Exists(Path.Join(WorkingDirectory.FullName, ".git"));
 
-	public void Fetch(string reference) =>
-		_ = ExecInWithRetry(
-			EnvironmentVars,
-			NetworkRetry,
-			"git",
-			"fetch",
-			"--no-tags",
-			"--prune",
-			"--no-recurse-submodules",
-			"--depth",
-			"1",
-			"origin",
-			reference
-		);
+	public void Fetch(string reference)
+	{
+		if (
+			!ExecInWithRetry(
+				EnvironmentVars,
+				NetworkRetry,
+				"git",
+				"fetch",
+				"--no-tags",
+				"--prune",
+				"--no-recurse-submodules",
+				"--depth",
+				"1",
+				"origin",
+				reference
+			)
+		)
+			throw new InvalidOperationException($"git fetch failed for '{reference}'");
+	}
 
 	public void EnableSparseCheckout(string[] folders) =>
 		ExecIn(EnvironmentVars, "git", ["sparse-checkout", "set", "--no-cone", .. folders]);
 
-	public void Checkout(string reference) => ExecIn(EnvironmentVars, "git", "checkout", "--force", reference);
+	public void Checkout(string reference)
+	{
+		if (!ExecInWithRetry(EnvironmentVars, RetryPolicy.None, "git", "checkout", "--force", reference))
+			throw new InvalidOperationException($"git checkout failed for '{reference}'");
+	}
 
 	public void GitAddOrigin(string origin) => ExecIn(EnvironmentVars, "git", "remote", "add", "origin", origin);
 }
diff --git a/tests/Navigation.Tests/Codex/CodexGitRepositoryTests.cs b/tests/Navigation.Tests/Codex/CodexGitRepositoryTests.cs
new file mode 100644
index 0000000000..d0ccc05f8b
--- /dev/null
+++ b/tests/Navigation.Tests/Codex/CodexGitRepositoryTests.cs
@@ -0,0 +1,77 @@
+// Licensed to Elasticsearch B.V under one or more agreements.
+// Elasticsearch B.V licenses this file to you under the Apache 2.0 License.
+// See the LICENSE file in the project root for more information
+
+using System.IO.Abstractions;
+using System.IO.Abstractions.TestingHelpers;
+using AwesomeAssertions;
+using Elastic.Codex.Sourcing;
+using Elastic.Documentation.Diagnostics;
+using Elastic.Documentation.ExternalCommands;
+using Microsoft.Extensions.Logging;
+using Microsoft.Extensions.Logging.Abstractions;
+
+namespace Elastic.Documentation.Navigation.Tests.Codex;
+
+public class CodexGitRepositoryTests
+{
+	[Fact]
+	public void Fetch_WhenGitFails_ThrowsWithoutLeavingTheFailureAsAnUncaughtJobError()
+	{
+		var gitCollector = new DiagnosticsCollector([]);
+		var git = CreateGit(gitCollector, ExitCode(128), ExitCode(128), ExitCode(128));
+
+		var act = () => git.Fetch("abc123");
+
+		act.Should().Throw<InvalidOperationException>().WithMessage("git fetch failed for 'abc123'");
+		gitCollector.Errors.Should().Be(1);
+	}
+
+	[Fact]
+	public void Checkout_WhenGitFails_ThrowsAfterRecordingTheFailureOnTheGitCollector()
+	{
+		var gitCollector = new DiagnosticsCollector([]);
+		var git = CreateGit(gitCollector, ExitCode(1));
+
+		var act = () => git.Checkout("FETCH_HEAD");
+
+		act.Should().Throw<InvalidOperationException>().WithMessage("git checkout failed for 'FETCH_HEAD'");
+		gitCollector.Errors.Should().Be(1);
+	}
+
+	private static Func<int> ExitCode(int code) => () => code;
+
+	private static ScriptedCodexGitRepository CreateGit(IDiagnosticsCollector gitCollector, params Func<int>[] steps)
+	{
+		var fileSystem = new MockFileSystem();
+		var workingDirectory = fileSystem.DirectoryInfo.New("/tmp/clone/repo");
+		workingDirectory.Create();
+		return new ScriptedCodexGitRepository(gitCollector, workingDirectory, steps);
+	}
+
+	private sealed class ScriptedCodexGitRepository(
+		IDiagnosticsCollector collector,
+		IDirectoryInfo workingDirectory,
+		Func<int>[] steps
+	) : CodexGitRepository(NullLoggerFactory.Instance, collector, workingDirectory)
+	{
+		private int _callCount;
+
+		protected override int ExecInCore(
+			Dictionary<string, string> environmentVars,
+			TimeSpan? attemptTimeout,
+			string binary,
+			params string[] args
+		)
+		{
+			if (_callCount >= steps.Length)
+				throw new InvalidOperationException($"Unexpected invocation {_callCount + 1}");
+			return steps[_callCount++]();
+		}
+
+		protected override void DelayBeforeRetry(TimeSpan delay)
+		{
+			// Tests must not wait on the production 5s fetch back-off.
+		}
+	}
+}
diff --git a/tests/Navigation.Tests/Navigation.Tests.csproj b/tests/Navigation.Tests/Navigation.Tests.csproj
index 7efb6503c1..ed92b1c5c4 100644
--- a/tests/Navigation.Tests/Navigation.Tests.csproj
+++ b/tests/Navigation.Tests/Navigation.Tests.csproj
@@ -9,6 +9,7 @@
 
   <ItemGroup>
     <ProjectReference Include="..\..\src\Elastic.Codex\Elastic.Codex.csproj"/>
+    <ProjectReference Include="..\..\src\Elastic.Documentation.Tooling\Elastic.Documentation.Tooling.csproj"/>
     <ProjectReference Include="..\..\src\Elastic.Documentation.Configuration\Elastic.Documentation.Configuration.csproj"/>
     <ProjectReference Include="..\..\src\Elastic.Documentation.Navigation\Elastic.Documentation.Navigation.csproj"/>
     <ProjectReference Include="..\..\src\Elastic.Documentation.ServiceDefaults\Elastic.Documentation.ServiceDefaults.csproj" />