diff --git a/.changeset/gold-eggs-check.md b/.changeset/gold-eggs-check.md
new file mode 100644
index 0000000000..e2b1104984
--- /dev/null
+++ b/.changeset/gold-eggs-check.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/workspace.manifest-writer": patch
+"pnpm": patch
+---
+
+Sort keys in `pnpm-workspace.yaml` with deep [#9701](https://github.com/pnpm/pnpm/pull/9701).
diff --git a/workspace/manifest-writer/src/index.ts b/workspace/manifest-writer/src/index.ts
index 85991e9cfd..52e89bf438 100644
--- a/workspace/manifest-writer/src/index.ts
+++ b/workspace/manifest-writer/src/index.ts
@@ -11,7 +11,7 @@ import { sortKeysByPriority } from '@pnpm/object.key-sorting'
 async function writeManifestFile (dir: string, manifest: Partial<WorkspaceManifest>): Promise<void> {
   manifest = sortKeysByPriority({
     priority: { packages: 0 },
-    deep: false,
+    deep: true,
   }, manifest)
   return writeYamlFile(path.join(dir, WORKSPACE_MANIFEST_FILENAME), manifest, {
     lineWidth: -1, // This is setting line width to never wrap