diff --git a/.changeset/warn-ignored-global-settings.md b/.changeset/warn-ignored-global-settings.md
new file mode 100644
index 0000000000..0c54c5a538
--- /dev/null
+++ b/.changeset/warn-ignored-global-settings.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/config.reader": patch
+"pnpm": patch
+---
+
+Print a warning when settings that are not allowed in the global config file (e.g. `nodeLinker`, `hoistPattern`) are present in `config.yaml` and silently ignored. Previously these settings were dropped without any feedback, leaving users unsure why their global configuration had no effect. The warning suggests moving those settings to a project-level `pnpm-workspace.yaml`, or sharing them across projects via [config dependencies](https://pnpm.io/11.x/config-dependencies).
diff --git a/config/reader/src/index.ts b/config/reader/src/index.ts
index 99dc431c78..ea0f486c09 100644
--- a/config/reader/src/index.ts
+++ b/config/reader/src/index.ts
@@ -290,11 +290,17 @@ export async function getConfig (opts: {
   // Reuse the global config.yaml already read for npmrcAuthFile
   const globalYamlConfig = globalYamlConfigForNpmrcAuthFile
   if (globalYamlConfig) {
+    const ignoredKeys: string[] = []
     for (const key in globalYamlConfig) {
       if (!isConfigFileKey(kebabCase(key))) {
+        ignoredKeys.push(key)
         delete globalYamlConfig[key as keyof typeof globalYamlConfig]
       }
     }
+    if (ignoredKeys.length > 0) {
+      const globalYamlConfigPath = path.join(configDir, GLOBAL_CONFIG_YAML_FILENAME)
+      warnings.push(`The following settings cannot be set in the global config file ("${globalYamlConfigPath}") and were ignored: ${ignoredKeys.map(k => `"${k}"`).join(', ')}. Move them to a project-level pnpm-workspace.yaml. To share these settings across projects, use config dependencies: https://pnpm.io/11.x/config-dependencies`)
+    }
     addSettingsFromWorkspaceManifestToConfig(pnpmConfig, {
       configFromCliOpts,
       projectManifest: undefined,
diff --git a/config/reader/test/index.ts b/config/reader/test/index.ts
index ce76763996..b405f13ff1 100644
--- a/config/reader/test/index.ts
+++ b/config/reader/test/index.ts
@@ -1687,6 +1687,44 @@ describe('global config.yaml', () => {
     expect(config.dangerouslyAllowAllBuilds).toBeDefined()
   })
 
+  test('warns when global config.yaml contains settings that are not allowed in the global config', async () => {
+    prepareEmpty()
+
+    fs.mkdirSync('.config/pnpm', { recursive: true })
+    writeYamlFileSync('.config/pnpm/config.yaml', {
+      dangerouslyAllowAllBuilds: true,
+      nodeLinker: 'hoisted',
+      hoistPattern: ['*eslint*'],
+    })
+
+    process.env.XDG_CONFIG_HOME = path.resolve('.config')
+
+    const { config, warnings } = await getConfig({
+      cliOptions: {},
+      packageManager: {
+        name: 'pnpm',
+        version: '1.0.0',
+      },
+      workspaceDir: process.cwd(),
+    })
+
+    // Allowed setting is still applied.
+    expect(config.dangerouslyAllowAllBuilds).toBe(true)
+    // Ignored settings do not leak into the config.
+    expect(config.nodeLinker).not.toBe('hoisted')
+    expect(config.hoistPattern).toEqual(['*'])
+
+    const warning = warnings.find((w) => w.includes('global config file'))
+    expect(warning).toBeDefined()
+    expect(warning).toContain('"nodeLinker"')
+    expect(warning).toContain('"hoistPattern"')
+    expect(warning).not.toContain('"dangerouslyAllowAllBuilds"')
+    expect(warning).toContain(path.join(process.env.XDG_CONFIG_HOME!, 'pnpm', 'config.yaml'))
+    expect(warning).toContain('pnpm-workspace.yaml')
+    expect(warning).toContain('https://pnpm.io/11.x/config-dependencies')
+    expect(warning).not.toContain('.npmrc')
+  })
+
   test('reads proxy settings from global config.yaml', async () => {
     prepareEmpty()