diff --git a/src/Elastic.Markdown/Myst/InlineParsers/DiagnosticLinkInlineParser.cs b/src/Elastic.Markdown/Myst/InlineParsers/DiagnosticLinkInlineParser.cs
index 0f2f1b614..1296d26f4 100644
--- a/src/Elastic.Markdown/Myst/InlineParsers/DiagnosticLinkInlineParser.cs
+++ b/src/Elastic.Markdown/Myst/InlineParsers/DiagnosticLinkInlineParser.cs
@@ -179,6 +179,9 @@ private static void ProcessCrossLink(LinkInline link, InlineProcessor processor,
 		if (url != null)
 			context.Build.Collector.EmitCrossLink(url);
 
+		// Store the original cross-link URL for LLM rendering
+		link.SetData("originalCrossLinkUrl", uri.ToString());
+
 		if (context.CrossLinkResolver.TryResolve(
 				s => processor.EmitError(link, s),
 				uri, out var resolvedUri)
diff --git a/src/Elastic.Markdown/Myst/Renderers/LlmMarkdown/LlmInlineRenderers.cs b/src/Elastic.Markdown/Myst/Renderers/LlmMarkdown/LlmInlineRenderers.cs
index 9ef11985d..58669639f 100644
--- a/src/Elastic.Markdown/Myst/Renderers/LlmMarkdown/LlmInlineRenderers.cs
+++ b/src/Elastic.Markdown/Myst/Renderers/LlmMarkdown/LlmInlineRenderers.cs
@@ -2,6 +2,7 @@
 // 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 Elastic.Markdown.IO;
 using Elastic.Markdown.Myst.InlineParsers.Substitution;
 using Elastic.Markdown.Myst.Roles;
 using Elastic.Markdown.Myst.Roles.Kbd;
@@ -32,8 +33,32 @@ protected override void Write(LlmMarkdownRenderer renderer, LinkInline obj)
 			renderer.WriteChildren(obj);
 			renderer.Writer.Write("](");
 			var url = obj.GetDynamicUrl?.Invoke() ?? obj.Url;
-			var absoluteUrl = LlmRenderingHelpers.MakeAbsoluteUrl(renderer, url);
-			renderer.Writer.Write(absoluteUrl ?? string.Empty);
+
+			// Check if this is an internal link to a markdown page
+			var isCrossLink = (obj.GetData("isCrossLink") as bool?) == true;
+			var hasTargetNavigationRoot = obj.GetData($"Target{nameof(MarkdownFile.NavigationRoot)}") != null;
+			var originalCrossLinkUrl = obj.GetData("originalCrossLinkUrl") as string;
+			var isInternalMarkdownLink = !isCrossLink && hasTargetNavigationRoot;
+			var isCrossLinkToMarkdown = isCrossLink && originalCrossLinkUrl is not null && IsCrossLinkToMarkdown(originalCrossLinkUrl);
+
+			if (isInternalMarkdownLink)
+			{
+				// For internal markdown links, preserve the .md extension
+				renderer.Writer.Write(EnsureMarkdownExtension(url) ?? string.Empty);
+			}
+			else if (isCrossLinkToMarkdown)
+			{
+				// For cross-links to markdown files, use absolute URL with .md extension
+				var absoluteUrl = LlmRenderingHelpers.MakeAbsoluteUrl(renderer, url);
+				var urlWithMdExtension = EnsureMarkdownExtension(absoluteUrl);
+				renderer.Writer.Write(urlWithMdExtension ?? string.Empty);
+			}
+			else
+			{
+				// For external links and non-markdown cross-links, make absolute
+				var absoluteUrl = LlmRenderingHelpers.MakeAbsoluteUrl(renderer, url);
+				renderer.Writer.Write(absoluteUrl ?? string.Empty);
+			}
 		}
 		if (!string.IsNullOrEmpty(obj.Title))
 		{
@@ -43,6 +68,43 @@ protected override void Write(LlmMarkdownRenderer renderer, LinkInline obj)
 		}
 		renderer.Writer.Write(")");
 	}
+
+	/// <summary>
+	/// Ensures the URL ends with .md extension for markdown links
+	/// </summary>
+	private static string? EnsureMarkdownExtension(string? url)
+	{
+		if (string.IsNullOrEmpty(url))
+			return url;
+
+		// If it already has .md extension, return as-is
+		if (url.EndsWith(".md", StringComparison.OrdinalIgnoreCase))
+			return url;
+
+		// Convert absolute paths to relative paths for markdown links
+		var processedUrl = url.StartsWith('/') ? url.TrimStart('/') : url;
+
+		// Add .md extension to internal markdown links
+		return processedUrl + ".md";
+	}
+
+	/// <summary>
+	/// Checks if a cross-link URL points to a markdown file
+	/// </summary>
+	private static bool IsCrossLinkToMarkdown(string originalCrossLinkUrl)
+	{
+		if (string.IsNullOrEmpty(originalCrossLinkUrl))
+			return false;
+
+		// Parse the cross-link URI to extract the path
+		if (Uri.TryCreate(originalCrossLinkUrl, UriKind.Absolute, out var uri))
+		{
+			var path = uri.AbsolutePath;
+			return path.EndsWith(".md", StringComparison.OrdinalIgnoreCase);
+		}
+
+		return false;
+	}
 }
 
 public class LlmEmphasisInlineRenderer : MarkdownObjectRenderer<LlmMarkdownRenderer, EmphasisInline>
diff --git a/tests/authoring/LlmMarkdown/LlmMarkdownOutput.fs b/tests/authoring/LlmMarkdown/LlmMarkdownOutput.fs
index 7daec9c86..21c18b47b 100644
--- a/tests/authoring/LlmMarkdown/LlmMarkdownOutput.fs
+++ b/tests/authoring/LlmMarkdown/LlmMarkdownOutput.fs
@@ -538,3 +538,27 @@ sub:
         markdown |> convertsToNewLLM """
 ## Hello, World!
 """
+
+type ``links`` () =
+    static let generator = Setup.Generate [
+        Index """
+This is a [link to another page](another-page.md).
+
+This is an [external link](https://example.com).
+
+This is a [cross-link](docs-content:/solutions/observability/apps/apm-server-binary.md).
+"""
+        Markdown "another-page.md" """
+# Another Page
+
+This is another page for testing internal links.
+"""
+    ]
+
+    [<Fact>]
+    let ``internal markdown links preserve .md extension while external links become absolute`` () =
+        generator |> convertsToNewLLM """
+This is a [link to another page](another-page.md).
+This is an [external link](https://example.com).
+This is a [cross-link](https://docs-v3-preview.elastic.dev/elastic/docs-content/tree/main/solutions/observability/apps/apm-server-binary.md).
+"""