diff --git a/.changeset/ignore-workspace-allow-builds.md b/.changeset/ignore-workspace-allow-builds.md
new file mode 100644
index 0000000000..0be6f9a06e
--- /dev/null
+++ b/.changeset/ignore-workspace-allow-builds.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/installing.commands": patch
+"pnpm": patch
+---
+
+Fixed `pnpm install --ignore-workspace` overwriting the `allowBuilds` map in `pnpm-workspace.yaml`. The ignored builds of a package with a build script were auto-populated into `allowBuilds` even though `--ignore-workspace` was passed, clobbering committed `true`/`false` values with the `set this to true or false` placeholder [#12469](https://github.com/pnpm/pnpm/issues/12469).
diff --git a/config/reader/src/Config.ts b/config/reader/src/Config.ts
index 1b2f818b1e..990fe8d217 100644
--- a/config/reader/src/Config.ts
+++ b/config/reader/src/Config.ts
@@ -232,6 +232,7 @@ export interface Config extends OptionsFromRootManifest {
   dedupePeerDependents?: boolean
   dedupePeers?: boolean
   patchesDir?: string
+  ignoreWorkspace?: boolean
   ignoreWorkspaceCycles?: boolean
   disallowWorkspaceCycles?: boolean
   packGzipLevel?: number
diff --git a/installing/commands/src/handleIgnoredBuilds.ts b/installing/commands/src/handleIgnoredBuilds.ts
index 3ca11963fc..207d4442b6 100644
--- a/installing/commands/src/handleIgnoredBuilds.ts
+++ b/installing/commands/src/handleIgnoredBuilds.ts
@@ -8,6 +8,7 @@ import { lexCompare } from '@pnpm/util.lex-comparator'
 
 export interface HandleIgnoredBuildsOpts {
   allowBuilds?: Record<string, boolean | string>
+  ignoreWorkspace?: boolean
   rootProjectManifestDir?: string
   workspaceDir?: string
   strictDepBuilds?: boolean
@@ -18,7 +19,9 @@ export async function handleIgnoredBuilds (
   ignoredBuilds: IgnoredBuilds | undefined
 ): Promise<void> {
   if (!ignoredBuilds?.size) return
-  await writeIgnoredBuildsToAllowBuilds(opts, ignoredBuilds)
+  if (!opts.ignoreWorkspace) {
+    await writeIgnoredBuildsToAllowBuilds(opts, ignoredBuilds)
+  }
   if (opts.strictDepBuilds) {
     throw new IgnoredBuildsError(ignoredBuilds)
   }
diff --git a/installing/commands/src/installDeps.ts b/installing/commands/src/installDeps.ts
index 0dea29ce91..0dfa07f519 100644
--- a/installing/commands/src/installDeps.ts
+++ b/installing/commands/src/installDeps.ts
@@ -117,6 +117,7 @@ export type InstallDepsOptions = Pick<Config,
 | 'workspaceDir'
 | 'workspacePackagePatterns'
 | 'extraEnv'
+| 'ignoreWorkspace'
 | 'ignoreWorkspaceCycles'
 | 'disallowWorkspaceCycles'
 | 'configDependencies'
diff --git a/installing/commands/test/handleIgnoredBuilds.ts b/installing/commands/test/handleIgnoredBuilds.ts
new file mode 100644
index 0000000000..a55b569642
--- /dev/null
+++ b/installing/commands/test/handleIgnoredBuilds.ts
@@ -0,0 +1,31 @@
+import fs from 'node:fs'
+import path from 'node:path'
+
+import { expect, test } from '@jest/globals'
+import { prepareEmpty } from '@pnpm/prepare'
+import type { DepPath } from '@pnpm/types'
+import { readYamlFileSync } from 'read-yaml-file'
+import { writeYamlFileSync } from 'write-yaml-file'
+
+import { handleIgnoredBuilds } from '../lib/handleIgnoredBuilds.js'
+
+test('handleIgnoredBuilds does not update pnpm-workspace.yaml when workspace is ignored', async () => {
+  prepareEmpty()
+
+  const workspaceManifestFile = path.resolve('pnpm-workspace.yaml')
+  const workspaceManifest = {
+    allowBuilds: {
+      esbuild: false,
+    },
+  }
+  writeYamlFileSync(workspaceManifestFile, workspaceManifest)
+  const workspaceManifestBefore = fs.readFileSync(workspaceManifestFile, 'utf8')
+
+  await handleIgnoredBuilds({
+    ignoreWorkspace: true,
+    rootProjectManifestDir: process.cwd(),
+  }, new Set(['esbuild@0.25.0' as DepPath]))
+
+  expect(fs.readFileSync(workspaceManifestFile, 'utf8')).toBe(workspaceManifestBefore)
+  expect(readYamlFileSync(workspaceManifestFile)).toStrictEqual(workspaceManifest)
+})
diff --git a/pnpm/test/install/lifecycleScripts.ts b/pnpm/test/install/lifecycleScripts.ts
index 928c57e841..af225406ac 100644
--- a/pnpm/test/install/lifecycleScripts.ts
+++ b/pnpm/test/install/lifecycleScripts.ts
@@ -333,6 +333,29 @@ test('auto-populated placeholders are merged with existing allowBuilds', async (
   expect(manifest?.allowBuilds?.['@pnpm.e2e/pre-and-postinstall-scripts-example']).toBe('set this to true or false')
 })
 
+test('install --ignore-workspace does not overwrite allowBuilds in pnpm-workspace.yaml', () => {
+  prepare({
+    dependencies: {
+      '@pnpm.e2e/pre-and-postinstall-scripts-example': '1.0.0',
+    },
+  })
+  writeYamlFileSync('pnpm-workspace.yaml', {
+    allowBuilds: {
+      '@pnpm.e2e/pre-and-postinstall-scripts-example': false,
+    },
+  })
+  const manifestBefore = fs.readFileSync('pnpm-workspace.yaml', 'utf8')
+
+  const { status, stdout, stderr } = execPnpmSync(['install', '--ignore-workspace'])
+
+  // The build is ignored (--ignore-workspace skips the allowBuilds entry), so the
+  // install ends in ERR_PNPM_IGNORED_BUILDS — the same code path that would have
+  // written the placeholder. The manifest must stay untouched regardless.
+  expect(status).toBe(1)
+  expect(`${stdout}${stderr}`).toContain('ERR_PNPM_IGNORED_BUILDS')
+  expect(fs.readFileSync('pnpm-workspace.yaml', 'utf8')).toBe(manifestBefore)
+})
+
 test('selective rebuild preserves ignoredBuilds for packages not being rebuilt', async () => {
   const project = prepare({})
   writeYamlFileSync('pnpm-workspace.yaml', {