diff --git a/.changeset/solid-suns-wear.md b/.changeset/solid-suns-wear.md
new file mode 100644
index 0000000000..ba2d77264c
--- /dev/null
+++ b/.changeset/solid-suns-wear.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-installation": patch
+"pnpm": patch
+---
+
+The parameter set by the `--allow-build` flag is written to `allowBuilds`.
diff --git a/exec/build-commands/test/approveBuilds.test.ts b/exec/build-commands/test/approveBuilds.test.ts
index 16192df72c..f84d43ae69 100644
--- a/exec/build-commands/test/approveBuilds.test.ts
+++ b/exec/build-commands/test/approveBuilds.test.ts
@@ -116,7 +116,8 @@ test('approve no builds', async () => {
 
   const manifest = readYamlFile<any>(path.resolve('pnpm-workspace.yaml')) // eslint-disable-line
   expect(manifest.onlyBuiltDependencies).toBeUndefined()
-  expect(manifest.ignoredBuiltDependencies?.sort()).toStrictEqual([
+  expect(manifest.ignoredBuiltDependencies).toBeUndefined()
+  expect(Object.keys(manifest.allowBuilds ?? {}).sort()).toStrictEqual([
     '@pnpm.e2e/install-script-example',
     '@pnpm.e2e/pre-and-postinstall-scripts-example',
   ])
@@ -147,8 +148,10 @@ test("works when root project manifest doesn't exist in a workspace", async () =
 
   expect(readYamlFile(workspaceManifestFile)).toStrictEqual({
     packages: ['packages/*'],
-    onlyBuiltDependencies: ['@pnpm.e2e/pre-and-postinstall-scripts-example'],
-    ignoredBuiltDependencies: ['@pnpm.e2e/install-script-example'],
+    allowBuilds: {
+      '@pnpm.e2e/install-script-example': false,
+      '@pnpm.e2e/pre-and-postinstall-scripts-example': true,
+    },
   })
 })
 
@@ -226,7 +229,9 @@ test('should approve builds with package.json that has no onlyBuiltDependencies
 
   expect(readYamlFile(workspaceManifestFile)).toStrictEqual({
     packages: ['packages/*'],
-    onlyBuiltDependencies: ['@pnpm.e2e/pre-and-postinstall-scripts-example'],
-    ignoredBuiltDependencies: ['@pnpm.e2e/install-script-example'],
+    allowBuilds: {
+      '@pnpm.e2e/install-script-example': false,
+      '@pnpm.e2e/pre-and-postinstall-scripts-example': true,
+    },
   })
 })
diff --git a/pnpm/test/install/lifecycleScripts.ts b/pnpm/test/install/lifecycleScripts.ts
index 877d3b29a9..850c3c55d9 100644
--- a/pnpm/test/install/lifecycleScripts.ts
+++ b/pnpm/test/install/lifecycleScripts.ts
@@ -186,7 +186,8 @@ test('selectively allow scripts in some dependencies by --allow-build flag', asy
   const manifest = loadJsonFileSync<ProjectManifest>('package.json')
   expect(manifest.pnpm?.onlyBuiltDependencies).toBeUndefined()
   const modulesManifest = await readWorkspaceManifest(project.dir())
-  expect(modulesManifest?.onlyBuiltDependencies).toStrictEqual(['@pnpm.e2e/install-script-example'])
+  expect(modulesManifest?.onlyBuiltDependencies).toBeUndefined()
+  expect(modulesManifest?.allowBuilds).toStrictEqual({ '@pnpm.e2e/install-script-example': true })
 })
 
 test('--allow-build flag should specify the package', async () => {
diff --git a/workspace/manifest-writer/src/index.ts b/workspace/manifest-writer/src/index.ts
index df449c99c7..cfacd3d463 100644
--- a/workspace/manifest-writer/src/index.ts
+++ b/workspace/manifest-writer/src/index.ts
@@ -47,7 +47,7 @@ export async function updateWorkspaceManifest (dir: string, opts: {
 
   // If the current manifest has allowBuilds, convert old fields to allowBuilds format
   const updatedFields = { ...opts.updatedFields }
-  if (manifest.allowBuilds != null && (updatedFields.onlyBuiltDependencies != null || updatedFields.ignoredBuiltDependencies != null)) {
+  if (manifest.allowBuilds != null || (manifest.onlyBuiltDependencies == null && manifest.ignoredBuiltDependencies == null)) {
     const allowBuilds: Record<string, boolean | string> = { ...manifest.allowBuilds }
 
     // Convert onlyBuiltDependencies to allowBuilds with true values
@@ -65,7 +65,9 @@ export async function updateWorkspaceManifest (dir: string, opts: {
     }
 
     // Update allowBuilds instead of the old fields
-    updatedFields.allowBuilds = allowBuilds
+    if (manifest.allowBuilds != null || Object.keys(allowBuilds).length > 0) {
+      updatedFields.allowBuilds = allowBuilds
+    }
     delete updatedFields.onlyBuiltDependencies
     delete updatedFields.ignoredBuiltDependencies
   }
diff --git a/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts b/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts
index 31a39995cf..6d45b3bcd6 100644
--- a/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts
+++ b/workspace/manifest-writer/test/updateWorkspaceManifest.test.ts
@@ -8,7 +8,7 @@ import { sync as writeYamlFile } from 'write-yaml-file'
 test('updateWorkspaceManifest adds a new setting', async () => {
   const dir = tempDir(false)
   const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
-  writeYamlFile(filePath, { packages: ['*'] })
+  writeYamlFile(filePath, { packages: ['*'], onlyBuiltDependencies: [] })
   await updateWorkspaceManifest(dir, {
     updatedFields: { onlyBuiltDependencies: [] },
   })