diff --git a/.changeset/allow-builds-pnpmfile-fix.md b/.changeset/allow-builds-pnpmfile-fix.md
new file mode 100644
index 0000000000..f166e27edb
--- /dev/null
+++ b/.changeset/allow-builds-pnpmfile-fix.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/cli-utils": patch
+"pnpm": patch
+---
+
+Fixed `allowBuilds` not working when set via `.pnpmfile.cjs` [#10516](https://github.com/pnpm/pnpm/issues/10516).
diff --git a/cli/cli-utils/src/getConfig.ts b/cli/cli-utils/src/getConfig.ts
index 562c580795..e2d0d661a7 100644
--- a/cli/cli-utils/src/getConfig.ts
+++ b/cli/cli-utils/src/getConfig.ts
@@ -116,4 +116,24 @@ function applyDerivedConfig (config: Config): void {
     delete config.hoistPattern
     delete config.publicHoistPattern
   }
+  if (config.allowBuilds) {
+    config.onlyBuiltDependencies ??= []
+    config.ignoredBuiltDependencies ??= []
+    const onlyBuiltSet = new Set(config.onlyBuiltDependencies)
+    const ignoredBuiltSet = new Set(config.ignoredBuiltDependencies)
+    for (const [packagePattern, build] of Object.entries(config.allowBuilds)) {
+      switch (build) {
+      case true:
+        if (!onlyBuiltSet.has(packagePattern)) {
+          config.onlyBuiltDependencies.push(packagePattern)
+        }
+        break
+      case false:
+        if (!ignoredBuiltSet.has(packagePattern)) {
+          config.ignoredBuiltDependencies.push(packagePattern)
+        }
+        break
+      }
+    }
+  }
 }
diff --git a/cli/cli-utils/test/getConfig.test.ts b/cli/cli-utils/test/getConfig.test.ts
index 245f46cdb1..148f8de1bc 100644
--- a/cli/cli-utils/test/getConfig.test.ts
+++ b/cli/cli-utils/test/getConfig.test.ts
@@ -42,3 +42,43 @@ test('hoist: false removes hoistPattern', async () => {
   expect(config.hoist).toBe(false)
   expect(config.hoistPattern).toBeUndefined()
 })
+
+test('allowBuilds populates onlyBuiltDependencies and ignoredBuiltDependencies', async () => {
+  prepare()
+
+  const config = await getConfig({
+    allowBuilds: {
+      'allowed-pkg': true,
+      'another-allowed': true,
+      'blocked-pkg': false,
+    },
+  }, {
+    workspaceDir: '.',
+    excludeReporter: false,
+    rcOptionsTypes: {},
+  })
+
+  expect(config.onlyBuiltDependencies).toContain('allowed-pkg')
+  expect(config.onlyBuiltDependencies).toContain('another-allowed')
+  expect(config.ignoredBuiltDependencies).toContain('blocked-pkg')
+})
+
+test('allowBuilds does not add duplicates', async () => {
+  prepare()
+
+  const config = await getConfig({
+    onlyBuiltDependencies: ['already-allowed'],
+    ignoredBuiltDependencies: ['already-blocked'],
+    allowBuilds: {
+      'already-allowed': true,
+      'already-blocked': false,
+    },
+  }, {
+    workspaceDir: '.',
+    excludeReporter: false,
+    rcOptionsTypes: {},
+  })
+
+  expect(config.onlyBuiltDependencies).toEqual(['already-allowed'])
+  expect(config.ignoredBuiltDependencies).toEqual(['already-blocked'])
+})