diff --git a/.changeset/fifty-trainers-unite.md b/.changeset/fifty-trainers-unite.md
new file mode 100644
index 0000000000..deb2b16bc5
--- /dev/null
+++ b/.changeset/fifty-trainers-unite.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/workspace.manifest-writer": patch
+"pnpm": patch
+---
+
+Fix the update of `pnpm-workspace.yaml` by the `pnpm approve-builds` command [#9168](https://github.com/pnpm/pnpm/issues/9168).
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index e070021ce5..999d346827 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -8048,6 +8048,9 @@ importers:
 
   workspace/manifest-writer:
     dependencies:
+      '@pnpm/constants':
+        specifier: workspace:*
+        version: link:../../packages/constants
       '@pnpm/workspace.read-manifest':
         specifier: workspace:*
         version: link:../read-manifest
@@ -8055,9 +8058,15 @@ importers:
         specifier: 'catalog:'
         version: 5.0.0
     devDependencies:
+      '@pnpm/prepare-temp-dir':
+        specifier: workspace:*
+        version: link:../../__utils__/prepare-temp-dir
       '@pnpm/workspace.manifest-writer':
         specifier: workspace:*
         version: 'link:'
+      read-yaml-file:
+        specifier: 'catalog:'
+        version: 2.1.0
 
   workspace/pkgs-graph:
     dependencies:
diff --git a/workspace/manifest-writer/package.json b/workspace/manifest-writer/package.json
index 83cc8168d5..000f96caac 100644
--- a/workspace/manifest-writer/package.json
+++ b/workspace/manifest-writer/package.json
@@ -12,10 +12,11 @@
     "node": ">=18.12"
   },
   "scripts": {
-    "lint": "eslint \"src/**/*.ts\"",
-    "test": "pnpm run compile",
+    "lint": "eslint \"src/**/*.ts\" \"test/**/*.ts\"",
+    "test": "pnpm run compile && pnpm run _test",
     "prepublishOnly": "pnpm run compile",
-    "compile": "tsc --build && pnpm run lint --fix"
+    "compile": "tsc --build && pnpm run lint --fix",
+    "_test": "jest"
   },
   "repository": "https://github.com/pnpm/pnpm/blob/main/workspace/manifest-writer",
   "keywords": [
@@ -28,12 +29,15 @@
   },
   "homepage": "https://github.com/pnpm/pnpm/blob/main/workspace/manifest-writer#readme",
   "dependencies": {
+    "@pnpm/constants": "workspace:*",
     "@pnpm/workspace.read-manifest": "workspace:*",
     "write-yaml-file": "catalog:"
   },
   "funding": "https://opencollective.com/pnpm",
   "devDependencies": {
-    "@pnpm/workspace.manifest-writer": "workspace:*"
+    "@pnpm/prepare-temp-dir": "workspace:*",
+    "@pnpm/workspace.manifest-writer": "workspace:*",
+    "read-yaml-file": "catalog:"
   },
   "exports": {
     ".": "./lib/index.js"
diff --git a/workspace/manifest-writer/src/index.ts b/workspace/manifest-writer/src/index.ts
index 61d29c3c3d..558a8b7089 100644
--- a/workspace/manifest-writer/src/index.ts
+++ b/workspace/manifest-writer/src/index.ts
@@ -1,10 +1,12 @@
+import path from 'path'
 import { readWorkspaceManifest, type WorkspaceManifest } from '@pnpm/workspace.read-manifest'
+import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
 import writeYamlFile from 'write-yaml-file'
 
 export async function updateWorkspaceManifest (dir: string, updatedFields: Partial<WorkspaceManifest>): Promise<void> {
   const manifest = await readWorkspaceManifest(dir)
-  await writeYamlFile(dir, {
+  await writeYamlFile(path.join(dir, WORKSPACE_MANIFEST_FILENAME), {
     ...manifest,
-    updatedFields,
+    ...updatedFields,
   })
 }
diff --git a/workspace/manifest-writer/test/tsconfig.json b/workspace/manifest-writer/test/tsconfig.json
new file mode 100644
index 0000000000..74036126c6
--- /dev/null
+++ b/workspace/manifest-writer/test/tsconfig.json
@@ -0,0 +1,17 @@
+{
+  "extends": "../tsconfig.json",
+  "compilerOptions": {
+    "noEmit": false,
+    "outDir": "../test.lib",
+    "rootDir": "."
+  },
+  "include": [
+    "**/*.ts",
+    "../../../__typings__/**/*.d.ts"
+  ],
+  "references": [
+    {
+      "path": ".."
+    }
+  ]
+}
diff --git a/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts b/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts
new file mode 100644
index 0000000000..497cbf6fe1
--- /dev/null
+++ b/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts
@@ -0,0 +1,19 @@
+import path from 'path'
+import { WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
+import { tempDir } from '@pnpm/prepare-temp-dir'
+import { updateWorkspaceManifest } from '@pnpm/workspace.manifest-writer'
+import { sync as readYamlFile } from 'read-yaml-file'
+import { sync as writeYamlFile } from 'write-yaml-file'
+
+test('updateWorkspaceManifest', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFile(filePath, { packages: ['*'] })
+  await updateWorkspaceManifest(dir, {
+    onlyBuiltDependencies: [],
+  })
+  expect(readYamlFile(filePath)).toStrictEqual({
+    packages: ['*'],
+    onlyBuiltDependencies: [],
+  })
+})
diff --git a/workspace/manifest-writer/tsconfig.json b/workspace/manifest-writer/tsconfig.json
index ef43e9ee20..aa058c6ff8 100644
--- a/workspace/manifest-writer/tsconfig.json
+++ b/workspace/manifest-writer/tsconfig.json
@@ -9,6 +9,12 @@
     "../../__typings__/**/*.d.ts"
   ],
   "references": [
+    {
+      "path": "../../__utils__/prepare-temp-dir"
+    },
+    {
+      "path": "../../packages/constants"
+    },
     {
       "path": "../read-manifest"
     }