diff --git a/.changeset/global-yaml-user-prefs.md b/.changeset/global-yaml-user-prefs.md
new file mode 100644
index 0000000000..76df43a3d4
--- /dev/null
+++ b/.changeset/global-yaml-user-prefs.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/config.reader": patch
+"pnpm": patch
+---
+
+Allow user-level preferences in the global `config.yaml`. The following settings can now be set in `~/.config/pnpm/config.yaml` (or via `pnpm config set --location global`) instead of being restricted to `pnpm-workspace.yaml`: `agent`, `globalVirtualStoreDir`, `initPackageManager`, `initType`, `registrySupportsTimeField`, `scriptShell`, `shellEmulator`, `sideEffectsCache`, `sideEffectsCacheReadonly`, `stateDir`, `strictDepBuilds`, `trustPolicy`, `trustPolicyExclude`, `trustPolicyIgnoreAfter`, `updateNotifier`, `useStderr`, `verifyDepsBeforeRun`, `verifyStoreIntegrity`, `virtualStoreDir`, `virtualStoreDirMaxLength` [#11474](https://github.com/pnpm/pnpm/issues/11474).
diff --git a/config/reader/src/configFileKey.ts b/config/reader/src/configFileKey.ts
index 7500aa4372..a1891e87a9 100644
--- a/config/reader/src/configFileKey.ts
+++ b/config/reader/src/configFileKey.ts
@@ -8,6 +8,7 @@ type PnpmKey = keyof typeof pnpmTypes
  * Keys from {@link pnpmTypes} that are valid fields in a global config file.
  */
 export const pnpmConfigFileKeys = [
+  'agent',
   'bail',
   'ci',
   'color',
@@ -28,7 +29,10 @@ export const pnpmConfigFileKeys = [
   'global-dir',
   'global-path',
   'global-pnpmfile',
+  'global-virtual-store-dir',
   'http-proxy',
+  'init-package-manager',
+  'init-type',
   'optimistic-repeat-install',
   'loglevel',
   'maxsockets',
@@ -47,10 +51,26 @@ export const pnpmConfigFileKeys = [
   'prefer-offline',
   'prefer-symlinked-executables',
   'block-exotic-subdeps',
+  'registry-supports-time-field',
   'reporter',
   'resolution-mode',
+  'script-shell',
+  'shell-emulator',
+  'side-effects-cache',
+  'side-effects-cache-readonly',
+  'state-dir',
   'store-dir',
+  'strict-dep-builds',
+  'trust-policy',
+  'trust-policy-exclude',
+  'trust-policy-ignore-after',
+  'update-notifier',
   'use-beta-cli',
+  'use-stderr',
+  'verify-deps-before-run',
+  'verify-store-integrity',
+  'virtual-store-dir',
+  'virtual-store-dir-max-length',
 ] as const satisfies readonly PnpmKey[]
 export type PnpmConfigFileKey = typeof pnpmConfigFileKeys[number]
 
@@ -87,8 +107,6 @@ export const excludedPnpmKeys = [
   'ignore-workspace-cycles',
   'ignore-workspace-root-check',
   'include-workspace-root',
-  'init-package-manager',
-  'init-type',
   'inject-workspace-packages',
   'legacy-dir-filtering',
   'link-workspace-packages',
@@ -104,7 +122,6 @@ export const excludedPnpmKeys = [
   'patches-dir',
   'pnpmfile',
   'pm-on-fail',
-  'agent',
   'prefer-workspace-packages',
   'preserve-absolute-paths',
   'production',
@@ -118,28 +135,13 @@ export const excludedPnpmKeys = [
   'save-catalog-name',
   'save-peer',
   'save-workspace-protocol',
-  'script-shell',
   'shamefully-hoist',
   'shared-workspace-lockfile',
-  'shell-emulator',
-  'side-effects-cache',
-  'side-effects-cache-readonly',
   'symlink',
   'sort',
-  'state-dir',
   'stream',
-  'strict-dep-builds',
   'strict-store-pkg-content-check',
   'strict-peer-dependencies',
-  'trust-policy',
-  'trust-policy-exclude',
-  'trust-policy-ignore-after',
-  'use-stderr',
-  'verify-deps-before-run',
-  'verify-store-integrity',
-  'global-virtual-store-dir',
-  'virtual-store-dir',
-  'virtual-store-dir-max-length',
   'virtual-store-only',
   'peers-suffix-max-length',
   'workspace-concurrency',
@@ -148,8 +150,6 @@ export const excludedPnpmKeys = [
   'test-pattern',
   'changed-files-ignore-pattern',
   'embed-readme',
-  'update-notifier',
-  'registry-supports-time-field',
   'fail-if-no-match',
   'sync-injected-deps-after-scripts',
   'cpu',
diff --git a/config/reader/test/index.ts b/config/reader/test/index.ts
index b405f13ff1..a4f3ebd6d5 100644
--- a/config/reader/test/index.ts
+++ b/config/reader/test/index.ts
@@ -1687,6 +1687,55 @@ describe('global config.yaml', () => {
     expect(config.dangerouslyAllowAllBuilds).toBeDefined()
   })
 
+  test('reads user-level preference settings from global config.yaml', async () => {
+    prepareEmpty()
+
+    fs.mkdirSync('.config/pnpm', { recursive: true })
+    writeYamlFileSync('.config/pnpm/config.yaml', {
+      scriptShell: '/usr/local/bin/bash',
+      shellEmulator: true,
+      updateNotifier: false,
+      stateDir: '/custom/state',
+      trustPolicy: 'no-downgrade',
+      trustPolicyExclude: ['legacy-pkg'],
+      registrySupportsTimeField: true,
+      sideEffectsCache: false,
+      strictDepBuilds: true,
+      useStderr: true,
+      verifyDepsBeforeRun: 'error',
+      verifyStoreIntegrity: false,
+      virtualStoreDir: '/custom/.pnpm',
+      virtualStoreDirMaxLength: 80,
+    })
+
+    process.env.XDG_CONFIG_HOME = path.resolve('.config')
+
+    const { config, warnings } = await getConfig({
+      cliOptions: {},
+      packageManager: {
+        name: 'pnpm',
+        version: '1.0.0',
+      },
+      workspaceDir: process.cwd(),
+    })
+
+    expect(config.scriptShell).toBe('/usr/local/bin/bash')
+    expect(config.shellEmulator).toBe(true)
+    expect(config.updateNotifier).toBe(false)
+    expect(config.stateDir).toBe('/custom/state')
+    expect(config.trustPolicy).toBe('no-downgrade')
+    expect(config.trustPolicyExclude).toEqual(['legacy-pkg'])
+    expect(config.registrySupportsTimeField).toBe(true)
+    expect(config.sideEffectsCache).toBe(false)
+    expect(config.strictDepBuilds).toBe(true)
+    expect(config.useStderr).toBe(true)
+    expect(config.verifyDepsBeforeRun).toBe('error')
+    expect(config.verifyStoreIntegrity).toBe(false)
+    expect(config.virtualStoreDir).toBe('/custom/.pnpm')
+    expect(config.virtualStoreDirMaxLength).toBe(80)
+    expect(warnings.find((w) => w.includes('global config file'))).toBeUndefined()
+  })
+
   test('warns when global config.yaml contains settings that are not allowed in the global config', async () => {
     prepareEmpty()