diff --git a/packages/guides/src/Compiler/Passes/GlobalMenuPass.php b/packages/guides/src/Compiler/Passes/GlobalMenuPass.php
index dac74b564..cbe9f4b18 100644
--- a/packages/guides/src/Compiler/Passes/GlobalMenuPass.php
+++ b/packages/guides/src/Compiler/Passes/GlobalMenuPass.php
@@ -62,8 +62,9 @@ public function run(array $documents, CompilerContextInterface $compilerContext)
         }
 
         $rootDocument = null;
+        $rootFile = $rootDocumentEntry->getFile();
         foreach ($documents as $document) {
-            if ($document->getDocumentEntry() === $rootDocumentEntry) {
+            if ($document->getDocumentEntry()->getFile() === $rootFile) {
                 $rootDocument = $document;
                 break;
             }
diff --git a/packages/guides/src/Compiler/Passes/ToctreeValidationPass.php b/packages/guides/src/Compiler/Passes/ToctreeValidationPass.php
index 75a69bb9b..ec93f9774 100644
--- a/packages/guides/src/Compiler/Passes/ToctreeValidationPass.php
+++ b/packages/guides/src/Compiler/Passes/ToctreeValidationPass.php
@@ -68,6 +68,7 @@ public function run(array $documents, CompilerContextInterface $compilerContext)
 
     public function isMissingInToctree(DocumentEntryNode $documentEntry, ProjectNode $projectNode): bool
     {
-        return $documentEntry->getParent() === null && $documentEntry !== $projectNode->getRootDocumentEntry();
+        return $documentEntry->getParent() === null
+            && $documentEntry->getFile() !== $projectNode->getRootDocumentEntry()->getFile();
     }
 }
diff --git a/packages/guides/src/Nodes/ProjectNode.php b/packages/guides/src/Nodes/ProjectNode.php
index 7690c434c..2afce43e2 100644
--- a/packages/guides/src/Nodes/ProjectNode.php
+++ b/packages/guides/src/Nodes/ProjectNode.php
@@ -47,7 +47,10 @@ final class ProjectNode extends CompoundNode
     /** @var array<string, array<string, InternalTarget>> */
     private array $internalLinkTargets = [];
 
-    /** @var DocumentEntryNode[] */
+    /** Cached root document entry for O(1) lookup */
+    private DocumentEntryNode|null $rootDocumentEntry = null;
+
+    /** @var array<string, DocumentEntryNode> */
     private array $documentEntries = [];
     private DateTimeImmutable $lastRendered;
 
@@ -182,6 +185,11 @@ public function getAllInternalTargets(): array
 
     public function addDocumentEntry(DocumentEntryNode $documentEntry): void
     {
+        // Cache root for O(1) lookup
+        if ($documentEntry->isRoot()) {
+            $this->rootDocumentEntry = $documentEntry;
+        }
+
         $this->documentEntries[$documentEntry->getFile()] = $documentEntry;
     }
 
@@ -193,10 +201,8 @@ public function getAllDocumentEntries(): array
 
     public function getRootDocumentEntry(): DocumentEntryNode
     {
-        foreach ($this->documentEntries as $documentEntry) {
-            if ($documentEntry->isRoot()) {
-                return $documentEntry;
-            }
+        if ($this->rootDocumentEntry !== null) {
+            return $this->rootDocumentEntry;
         }
 
         throw new Exception('No root document entry was found');
@@ -205,10 +211,9 @@ public function getRootDocumentEntry(): DocumentEntryNode
     /** @throws DocumentEntryNotFound */
     public function getDocumentEntry(string $file): DocumentEntryNode
     {
-        foreach ($this->documentEntries as $documentEntry) {
-            if ($documentEntry->getFile() === $file) {
-                return $documentEntry;
-            }
+        // O(1) lookup by file path
+        if (isset($this->documentEntries[$file])) {
+            return $this->documentEntries[$file];
         }
 
         throw new DocumentEntryNotFound('No document Entry found for file ' . $file);
@@ -217,7 +222,12 @@ public function getDocumentEntry(string $file): DocumentEntryNode
     /** @param DocumentEntryNode[] $documentEntries */
     public function setDocumentEntries(array $documentEntries): void
     {
-        $this->documentEntries = $documentEntries;
+        $this->documentEntries = [];
+        $this->rootDocumentEntry = null;
+
+        foreach ($documentEntries as $entry) {
+            $this->addDocumentEntry($entry);
+        }
     }
 
     public function findDocumentEntry(string $filePath): DocumentEntryNode|null
@@ -228,6 +238,7 @@ public function findDocumentEntry(string $filePath): DocumentEntryNode|null
     public function reset(): void
     {
         $this->documentEntries = [];
+        $this->rootDocumentEntry = null;
     }
 
     public function getLastRendered(): DateTimeImmutable
diff --git a/packages/guides/src/RenderContext.php b/packages/guides/src/RenderContext.php
index bc8e52b64..5d797667e 100644
--- a/packages/guides/src/RenderContext.php
+++ b/packages/guides/src/RenderContext.php
@@ -222,8 +222,9 @@ public function getProjectNode(): ProjectNode
 
     public function getDocumentNodeForEntry(DocumentEntryNode $entryNode): DocumentNode
     {
+        $file = $entryNode->getFile();
         foreach ($this->allDocuments as $child) {
-            if ($child->getDocumentEntry() === $entryNode) {
+            if ($child->getDocumentEntry()->getFile() === $file) {
                 return $child;
             }
         }
diff --git a/packages/guides/src/Renderer/DocumentTreeIterator.php b/packages/guides/src/Renderer/DocumentTreeIterator.php
index 30266415d..d2904dc5c 100644
--- a/packages/guides/src/Renderer/DocumentTreeIterator.php
+++ b/packages/guides/src/Renderer/DocumentTreeIterator.php
@@ -41,8 +41,9 @@ public function __construct(
 
     public function current(): DocumentNode
     {
+        $file = $this->levelNodes[$this->position]->getFile();
         foreach ($this->documents as $document) {
-            if ($document->getDocumentEntry() === $this->levelNodes[$this->position]) {
+            if ($document->getDocumentEntry()->getFile() === $file) {
                 return $document;
             }
         }
diff --git a/tests/Functional/FunctionalTest.php b/tests/Functional/FunctionalTest.php
index f0e5d53df..bcac5797f 100644
--- a/tests/Functional/FunctionalTest.php
+++ b/tests/Functional/FunctionalTest.php
@@ -25,10 +25,8 @@
 use phpDocumentor\Guides\Compiler\Compiler;
 use phpDocumentor\Guides\Compiler\CompilerContext;
 use phpDocumentor\Guides\NodeRenderers\NodeRenderer;
-use phpDocumentor\Guides\Nodes\DocumentTree\DocumentEntryNode;
 use phpDocumentor\Guides\Nodes\Node;
 use phpDocumentor\Guides\Nodes\ProjectNode;
-use phpDocumentor\Guides\Nodes\TitleNode;
 use phpDocumentor\Guides\Parser;
 use phpDocumentor\Guides\RenderContext;
 use phpDocumentor\Guides\Settings\ProjectSettings;
@@ -110,13 +108,11 @@ public function testFunctional(
 
             $parser = $this->getContainer()->get(Parser::class);
             assert($parser instanceof Parser);
-            $document = $parser->parse($rst);
-            $documentEntry = new DocumentEntryNode($document->getFilePath(), $document->getTitle() ?? TitleNode::fromString(''), true);
+            $document = $parser->parse($rst)->withIsRoot(true);
 
             $compiler = $this->getContainer()->get(Compiler::class);
             assert($compiler instanceof Compiler);
             $projectNode = new ProjectNode();
-            $projectNode->setDocumentEntries([$documentEntry]);
             $compiler->run([$document], new CompilerContext($projectNode));
 
             $inputFilesystem = FlySystemAdapter::createFromFileSystem(new Filesystem(new InMemoryFilesystemAdapter()));