diff --git a/sources/nodeUtils.ts b/sources/nodeUtils.ts
index c83f59bb9..36e8c8164 100644
--- a/sources/nodeUtils.ts
+++ b/sources/nodeUtils.ts
@@ -52,3 +52,59 @@ export function readPackageJson(content: string) {
     indent: getIndent(content),
   };
 }
+
+export function setPackageManager(content: string, packageManager: string) {
+  const {data, indent} = readPackageJson(content);
+  const value = JSON.stringify(packageManager);
+
+  if (content === ``)
+    return normalizeLineEndings(content, `${JSON.stringify({packageManager}, null, indent)}\n`);
+
+  if (typeof data !== `object` || data === null || Array.isArray(data))
+    throw new TypeError(`Expected package.json to contain an object`);
+
+  const edits: Array<{start: number, end: number}> = [];
+  let depth = 0;
+  let name: string | undefined;
+  let valueStart = -1;
+  let lastTokenEnd = 0;
+
+  // JSON.parse above validates the input. Tokenize strings as a whole so that
+  // escaped quotes and punctuation inside them cannot affect nesting depth.
+  for (const match of content.matchAll(/"(?:\\.|[^"\\])*"|[^\s]/g)) {
+    const token = match[0];
+    if (depth === 1) {
+      if (token === `,` || token === `}`) {
+        if (name === `packageManager`)
+          edits.push({start: valueStart, end: lastTokenEnd});
+
+        name = undefined;
+        valueStart = -1;
+      } else if (name === undefined) {
+        name = JSON.parse(token);
+      } else if (token !== `:` && valueStart === -1) {
+        valueStart = match.index;
+      }
+
+      if (token === `}`) {
+        break;
+      }
+    }
+
+    if (token === `{` || token === `[`) depth++;
+    if (token === `}` || token === `]`) depth--;
+    lastTokenEnd = match.index + token.length;
+  }
+
+  if (edits.length > 0) {
+    // Update duplicate keys too, without touching similarly named nested keys.
+    for (const {start, end} of edits.reverse())
+      content = content.slice(0, start) + value + content.slice(end);
+
+    return content;
+  }
+
+  const separator = Object.keys(data).length > 0 ? `,` : ``;
+  const spacing = /\r?\n/.test(content.slice(0, content.lastIndexOf(`}`))) ? `${getEndOfLine(content)}${indent}` : ``;
+  return `${content.slice(0, lastTokenEnd)}${separator}${spacing}"packageManager": ${value}${content.slice(lastTokenEnd)}`;
+}
diff --git a/sources/specUtils.ts b/sources/specUtils.ts
index 275c49058..d25d58e53 100644
--- a/sources/specUtils.ts
+++ b/sources/specUtils.ts
@@ -143,12 +143,10 @@ export async function setLocalPackageManager(cwd: string, info: PreparedPackageM
     ? await fs.promises.readFile(lookup.target, `utf8`)
     : ``;
 
-  const {data, indent} = nodeUtils.readPackageJson(content);
+  const {data} = nodeUtils.readPackageJson(content);
 
   const previousPackageManager = data.packageManager ?? (devEnginesValue ? `${devEnginesValue.name}@${devEnginesValue.version ?? `*`}` : `unknown`);
-  data.packageManager = `${info.locator.name}@${info.locator.reference}`;
-
-  const newContent = nodeUtils.normalizeLineEndings(content, `${JSON.stringify(data, null, indent)}\n`);
+  const newContent = nodeUtils.setPackageManager(content, `${info.locator.name}@${info.locator.reference}`);
   await fs.promises.writeFile(lookup.target, newContent, `utf8`);
 
   return {
diff --git a/tests/Use.test.ts b/tests/Use.test.ts
index 6dd37939e..532f69c6f 100644
--- a/tests/Use.test.ts
+++ b/tests/Use.test.ts
@@ -17,6 +17,33 @@ beforeEach(async () => {
 });
 
 describe(`UseCommand`, () => {
+  it.each([
+    {command: [`use`, `pnpm@1.9998.9999`], existing: false},
+    {command: [`use`, `pnpm@1.9998.9999`], existing: true},
+    {command: [`up`], existing: true},
+    {command: [`pnpm`, `--version`], existing: false},
+  ])(`preserves manifest formatting with $command (existing: $existing)`, async ({command, existing}) => {
+    process.env.AUTH_TYPE = `COREPACK_NPM_TOKEN`;
+    process.env.TEST_INTEGRITY = `valid`;
+    process.env.COREPACK_DEFAULT_TO_LATEST = `1`;
+    process.env.COREPACK_ENABLE_AUTO_PIN = `1`;
+
+    await xfs.mktempPromise(async cwd => {
+      const manifest = ppath.join(cwd, `package.json`);
+      const before = `{\r\n\t"name" : "example",\r\n\r\n\t"scripts": {"test": "echo ok"}${existing ? `,\r\n\t"packageManager" : "pnpm@1.0.0"` : ``}\r\n}\r\n`;
+      await xfs.writeFilePromise(manifest, before);
+
+      await expect(runCli(cwd, command, true)).resolves.toMatchObject({exitCode: 0});
+
+      const after = await xfs.readFilePromise(manifest, `utf8`);
+      const {packageManager} = JSON.parse(after);
+      expect(packageManager).toMatch(/^pnpm@1\.9998\.9999\+sha512\.[0-9a-f]{128}$/);
+      expect(after).toBe(existing
+        ? before.replace(`pnpm@1.0.0`, packageManager)
+        : before.replace(`}\r\n}`, `},\r\n\t"packageManager": "${packageManager}"\r\n}`));
+    });
+  });
+
   describe(`should set the package manager in the current project`, () => {
     it(`With an existing 'packageManager' field`, async () => {
       await xfs.mktempPromise(async cwd => {
diff --git a/tests/nodeUtils.test.ts b/tests/nodeUtils.test.ts
new file mode 100644
index 000000000..194cd0ab5
--- /dev/null
+++ b/tests/nodeUtils.test.ts
@@ -0,0 +1,58 @@
+import {describe, expect, it} from 'vitest';
+
+import {setPackageManager}    from '../sources/nodeUtils.ts';
+
+describe(`setPackageManager`, () => {
+  const version = `pnpm@9.0.0+sha512.abc`;
+  const value = JSON.stringify(version);
+
+  it.each([`\n`, `\r\n`])(`preserves blank lines and unrelated values with %j line endings`, eol => {
+    const before = [
+      `{`,
+      `\t"name" : "example",`,
+      ``,
+      `\t"scripts": {"test": "echo \\"ok\\""},`,
+      `\t"number": 1e+2,`,
+      ``,
+      `\t"dependencies": {`,
+      `\t\t"a": "1",`,
+      ``,
+      `\t\t"b": "2"`,
+      `\t}`,
+      ``,
+      `}`,
+      ``,
+    ].join(eol);
+    const expected = before.replace(`${eol}\t}${eol}`, `${eol}\t},${eol}\t"packageManager": ${value}${eol}`);
+
+    expect(setPackageManager(before, version)).toBe(expected);
+    expect(JSON.parse(expected).packageManager).toBe(version);
+  });
+
+  it.each([`"old"`, `null`, `false`, `123`, `[]`, `{"nested": ["}", {"packageManager": "untouched"}]}`])(`replaces an existing %s value without reformatting`, old => {
+    const before = `{\n  "name": "example",\n\n  "packageManager" : ${old}  ,\n  "private": true\n}`;
+    expect(setPackageManager(before, version)).toBe(before.replace(`: ${old}`, `: ${value}`));
+  });
+
+  it(`recognizes escaped and duplicate top-level keys`, () => {
+    const before = `{"packageManager":"first", "package\\u004danager": ["last"]}`;
+    expect(setPackageManager(before, version)).toBe(`{"packageManager":${value}, "package\\u004danager": ${value}}`);
+  });
+
+  it(`does not replace nested keys or punctuation inside strings`, () => {
+    const before = `{"nested":[{"packageManager":"old"}],"text":"\\"},[packageManager"}`;
+    expect(setPackageManager(before, version)).toBe(`${before.slice(0, -1)},"packageManager": ${value}}`);
+  });
+
+  it.each([`{}`, `{}\n`, `{}\r\n`, `{  }`, `\uFEFF{}\n`])(`preserves whitespace around an empty object %j`, before => {
+    expect(setPackageManager(before, version)).toBe(before.replace(`{`, `{"packageManager": ${value}`));
+  });
+
+  it(`creates a new manifest`, () => {
+    expect(JSON.parse(setPackageManager(``, version))).toEqual({packageManager: version});
+  });
+
+  it(`rejects invalid JSON before editing`, () => {
+    expect(() => setPackageManager(`{"name": }`, version)).toThrow(SyntaxError);
+  });
+});