diff --git a/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/modified.yaml b/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/modified.yaml
new file mode 100644
index 00000000000..27918e1dfea
--- /dev/null
+++ b/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/modified.yaml
@@ -0,0 +1,9 @@
+# This is an example of a package.yaml file with comments.
+
+  # pnpm should keep comments at the same indentation level
+  name: 'foo'
+  version: '1.0.0' # it should keep in-line comments on the same line
+  # It should allow in-line comments with no other content
+  type: 'commonjs'
+
+# And it should preserve comments at the end of the file. Note no newline.
diff --git a/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/package.yaml b/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/package.yaml
new file mode 100644
index 00000000000..f608f225c84
--- /dev/null
+++ b/pkg-manifest/read-project-manifest/fixtures/commented-package-yaml/package.yaml
@@ -0,0 +1,9 @@
+# This is an example of a package.yaml file with comments.
+
+  # pnpm should keep comments at the same indentation level
+  name: 'foo'
+  version: '1.0.0' # it should keep in-line comments on the same line
+  # It should allow in-line comments with no other content
+  type: 'module'
+
+# And it should preserve comments at the end of the file. Note no newline.
diff --git a/pkg-manifest/read-project-manifest/src/index.ts b/pkg-manifest/read-project-manifest/src/index.ts
index 9c4f924c032..bd7e293430b 100644
--- a/pkg-manifest/read-project-manifest/src/index.ts
+++ b/pkg-manifest/read-project-manifest/src/index.ts
@@ -4,12 +4,12 @@ import { PnpmError } from '@pnpm/error'
 import { type ProjectManifest } from '@pnpm/types'
 import { extractComments, type CommentSpecifier } from '@pnpm/text.comments-parser'
 import { writeProjectManifest } from '@pnpm/write-project-manifest'
-import readYamlFile from 'read-yaml-file'
 import detectIndent from '@gwhitney/detect-indent'
 import equal from 'fast-deep-equal'
 import isWindows from 'is-windows'
 import sortKeys from 'sort-keys'
 import {
+  readYamlFile,
   readJson5File,
   readJsonFile,
 } from './readFile'
@@ -86,11 +86,15 @@ export async function tryReadProjectManifest (projectDir: string): Promise<{
   }
   try {
     const manifestPath = path.join(projectDir, 'package.yaml')
-    const manifest = await readPackageYaml(manifestPath)
+    const { data, text } = await readPackageYaml(manifestPath)
     return {
       fileName: 'package.yaml',
-      manifest,
-      writeProjectManifest: createManifestWriter({ initialManifest: manifest, manifestPath }),
+      manifest: data,
+      writeProjectManifest: createManifestWriter({ //initialManifest: data, manifestPath }),
+        ...detectFileFormatting(text), //AndComments(text),
+        initialManifest: data,
+        manifestPath,
+      })
     }
   } catch (err: any) { // eslint-disable-line
     if (err.code !== 'ENOENT') throw err
@@ -160,10 +164,14 @@ export async function readExactProjectManifest (manifestPath: string) {
     }
   }
   case 'package.yaml': {
-    const manifest = await readPackageYaml(manifestPath)
+    const { data, text } = await readPackageYaml(manifestPath)
     return {
-      manifest,
-      writeProjectManifest: createManifestWriter({ initialManifest: manifest, manifestPath }),
+      manifest: data,
+      writeProjectManifest: createManifestWriter({ //initialManifest: manifest, manifestPath }),
+        ...detectFileFormatting(text), //AndComments(text),
+        initialManifest: data,
+        manifestPath,
+      }),
     }
   }
   }
diff --git a/pkg-manifest/read-project-manifest/src/readFile.ts b/pkg-manifest/read-project-manifest/src/readFile.ts
index 6a92cd5ddd9..e7bb692f4a7 100644
--- a/pkg-manifest/read-project-manifest/src/readFile.ts
+++ b/pkg-manifest/read-project-manifest/src/readFile.ts
@@ -1,9 +1,24 @@
 import gfs from '@pnpm/graceful-fs'
 import { type ProjectManifest } from '@pnpm/types'
+import YAML from 'yaml'
 import JSON5 from 'json5'
 import parseJson from 'parse-json'
 import stripBom from 'strip-bom'
 
+export async function readYamlFile (filePath: string) {
+  const text = await readFileWithoutBom(filePath)
+  try {
+    return {
+      data: YAML.parseDocument(text),
+      text,
+    }
+  } catch (err: any) { // eslint-disable-line
+    err.message = `${err.message as string} in ${filePath}`
+    err['code'] = 'ERR_PNPM_YAML_PARSE'
+    throw err
+  }
+}
+
 export async function readJson5File (filePath: string) {
   const text = await readFileWithoutBom(filePath)
   try {
diff --git a/pkg-manifest/read-project-manifest/test/index.ts b/pkg-manifest/read-project-manifest/test/index.ts
index 1f4959d29c9..76b54f58234 100644
--- a/pkg-manifest/read-project-manifest/test/index.ts
+++ b/pkg-manifest/read-project-manifest/test/index.ts
@@ -101,6 +101,26 @@ test('preserve comments in json5 file', async () => {
   const resultingManifest = await fs.readFile('package.json5', 'utf8')
   expect(resultingManifest).toBe(modifiedManifest)
 })
+/* FIXME
+test('preserve comments in YAML file', async () => {
+  const originalManifest = await fs.readFile(
+    path.join(fixtures, 'commented-package-yaml/package.yaml'), 'utf8')
+  const modifiedManifest = await fs.readFile(
+    path.join(fixtures, 'commented-package-yaml/modified.yaml'), 'utf8')
+
+  process.chdir(tempy.directory())
+  await fs.writeFile('package.yaml', originalManifest, 'utf8')
+
+  const { manifest, writeProjectManifest } = await readProjectManifest(process.cwd())
+
+  // Have to make a change to get it to write anything:
+  const newManifest = Object.assign({}, manifest, { type: 'commonjs' })
+
+  await writeProjectManifest(newManifest)
+
+  const resultingManifest = await fs.readFile('package.yaml', 'utf8')
+  expect(resultingManifest).toBe(modifiedManifest)
+})*/
 
 test('do not save manifest if it had no changes', async () => {
   process.chdir(tempy.directory())
diff --git a/pkg-manifest/write-project-manifest/src/index.ts b/pkg-manifest/write-project-manifest/src/index.ts
index ffedeca4434..3d1a59c9a86 100644
--- a/pkg-manifest/write-project-manifest/src/index.ts
+++ b/pkg-manifest/write-project-manifest/src/index.ts
@@ -2,13 +2,16 @@ import { promises as fs } from 'fs'
 import path from 'path'
 import { insertComments, type CommentSpecifier } from '@pnpm/text.comments-parser'
 import { type ProjectManifest } from '@pnpm/types'
+import YAML from 'yaml'
 import JSON5 from 'json5'
 import writeFileAtomic from 'write-file-atomic'
-import writeYamlFile from 'write-yaml-file'
 
 const YAML_FORMAT = {
-  noCompatMode: true,
-  noRefs: true,
+  //noCompatMode: true, // TODO don't try to be compatible with older yaml versions
+  //noRefs: true, // TODO don't convert duplicate objects into references
+  //indent: 2,
+  //indentSeq: false,
+  //singleQuote: false,
 }
 
 export async function writeProjectManifest (
@@ -20,12 +23,13 @@ export async function writeProjectManifest (
     insertFinalNewline?: boolean
   }
 ): Promise<void> {
+  await fs.mkdir(path.dirname(filePath), { recursive: true })
   const fileType = filePath.slice(filePath.lastIndexOf('.') + 1).toLowerCase()
   if (fileType === 'yaml') {
-    return writeYamlFile(filePath, manifest, YAML_FORMAT)
+    const yaml = YAML.stringify(manifest, YAML_FORMAT)
+    return writeFileAtomic(filePath, yaml)
   }
 
-  await fs.mkdir(path.dirname(filePath), { recursive: true })
   const trailingNewline = opts?.insertFinalNewline === false ? '' : '\n'
   const indent = opts?.indent ?? '\t'