diff --git a/src/Elastic.Markdown/IO/DocumentationSet.cs b/src/Elastic.Markdown/IO/DocumentationSet.cs
index aeae90851..5dc9886c4 100644
--- a/src/Elastic.Markdown/IO/DocumentationSet.cs
+++ b/src/Elastic.Markdown/IO/DocumentationSet.cs
@@ -189,6 +189,8 @@ public DocumentationSet(
 
 		Tree = new TableOfContentsTree(Source, Context, lookups, treeCollector, ref fileIndex);
 
+		var navigationIndex = 0;
+		UpdateNavigationIndex(Tree.NavigationItems, ref navigationIndex);
 		var markdownFiles = Files.OfType<MarkdownFile>().ToArray();
 
 		var excludedChildren = markdownFiles.Where(f => !f.PartOfNavigation).ToArray();
@@ -210,6 +212,28 @@ public DocumentationSet(
 		ValidateRedirectsExists();
 	}
 
+	private void UpdateNavigationIndex(IReadOnlyCollection<INavigationItem> navigationItems, ref int navigationIndex)
+	{
+		foreach (var item in navigationItems)
+		{
+			switch (item)
+			{
+				case FileNavigationItem fileNavigationItem:
+					var fileIndex = Interlocked.Increment(ref navigationIndex);
+					fileNavigationItem.NavigationIndex = fileIndex;
+					break;
+				case DocumentationGroup documentationGroup:
+					var groupIndex = Interlocked.Increment(ref navigationIndex);
+					documentationGroup.NavigationIndex = groupIndex;
+					UpdateNavigationIndex(documentationGroup.NavigationItems, ref navigationIndex);
+					break;
+				default:
+					Context.EmitError(Context.ConfigurationPath, $"Unhandled navigation item type: {item.GetType()}");
+					break;
+			}
+		}
+	}
+
 	public FrozenDictionary<int, INavigationItem> NavigationIndexedByOrder { get; }
 
 	private static IReadOnlyCollection<INavigationItem> CreateNavigationLookup(INavigationItem item)
diff --git a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
index fd7554c85..038b857be 100644
--- a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
+++ b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
@@ -99,7 +99,15 @@ out List<INavigationItem> navigationItems
 		groups = [];
 		navigationItems = [];
 		files = [];
+		var fileReferences = lookups.TableOfContents.OfType<FileReference>().ToArray();
 		var indexFile = virtualIndexFile;
+		FileReference? indexReference = null;
+		if (indexFile is null)
+		{
+			indexReference =
+				fileReferences.FirstOrDefault(f => f.RelativePath.EndsWith("index.md"))
+				?? fileReferences.FirstOrDefault();
+		}
 
 		var list = navigationItems;
 
@@ -158,8 +166,10 @@ void AddToNavigationItems(INavigationItem item, ref int fileIndex)
 				}
 
 				files.Add(md);
-				if (file.RelativePath.EndsWith("index.md") && d is MarkdownFile i)
-					indexFile ??= i;
+				if (file.RelativePath.EndsWith("index.md"))
+					indexFile ??= md;
+				else if (indexReference == file)
+					indexFile ??= md;
 
 				// Add the page to navigation items unless it's the index file
 				// the index file can either be the discovered `index.md` or the parent group's
diff --git a/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs b/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
index 7ea6727d8..12f072c5e 100644
--- a/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
+++ b/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
@@ -153,7 +153,8 @@ public async Task ParsesReferences()
 
 		var navigation = new GlobalNavigation(assembleSources, navigationFile);
 		var referenceNav = navigation.NavigationLookup[expectedRoot];
-		navigation.NavigationItems.Should().HaveSameCount(navigation.NavigationLookup);
+		navigation.NavigationItems.OfType<TableOfContentsTree>()
+			.Should().HaveSameCount(navigation.NavigationLookup);
 
 		referenceNav.Should().NotBeNull();
 		var navigationLookup = referenceNav.NavigationItems.OfType<TableOfContentsTree>().ToDictionary(i => i.Source, i => i);
@@ -314,11 +315,11 @@ public async Task UriResolving()
 		var resolvedUri = uriResolver.Resolve(new Uri("docs-content://reference/apm/something.md"), "/reference/apm/something");
 		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/apm/something");
 
-		resolvedUri = uriResolver.Resolve(new Uri("apm-agent-ios://reference/instrumentation.md"), "/reference/instrumentation");
-		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/apm/agents/ios/instrumentation");
+		resolvedUri = uriResolver.Resolve(new Uri("apm-agent-nodejs://reference/instrumentation.md"), "/reference/instrumentation");
+		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/apm/agents/nodejs/instrumentation");
 
-		resolvedUri = uriResolver.Resolve(new Uri("apm-agent-android://reference/a/file.md"), "/reference/a/file");
-		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/apm/agents/android/a/file");
+		resolvedUri = uriResolver.Resolve(new Uri("apm-agent-dotnet://reference/a/file.md"), "/reference/a/file");
+		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/apm/agents/dotnet/a/file");
 
 		resolvedUri = uriResolver.Resolve(new Uri("elasticsearch-net://reference/b/file.md"), "/reference/b/file");
 		resolvedUri.Should().Be("https://www.elastic.co/docs/reference/elasticsearch/clients/dotnet/b/file");