diff --git a/.changeset/warn-deprecated-pnpm-field-11677.md b/.changeset/warn-deprecated-pnpm-field-11677.md
new file mode 100644
index 0000000000..0c177c42ea
--- /dev/null
+++ b/.changeset/warn-deprecated-pnpm-field-11677.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/config.reader": patch
+"pnpm": patch
+---
+
+Warn when `package.json` contains a legacy `pnpm` field with settings pnpm no longer reads from `package.json` (e.g. `pnpm.overrides`, `pnpm.patchedDependencies`). Previously these were silently ignored after the upgrade from v10, leaving users unaware that their overrides/patched dependencies had stopped taking effect [#11677](https://github.com/pnpm/pnpm/issues/11677).
diff --git a/config/reader/src/index.ts b/config/reader/src/index.ts
index b0cc36a4ef..1d8eb41f37 100644
--- a/config/reader/src/index.ts
+++ b/config/reader/src/index.ts
@@ -404,6 +404,10 @@ export async function getConfig (opts: {
       if (pnpmConfig.rootProjectManifest.workspaces?.length && !pnpmConfig.workspaceDir) {
         warnings.push('The "workspaces" field in package.json is not supported by pnpm. Create a "pnpm-workspace.yaml" file instead.')
       }
+      const ignoredPnpmFieldKeys = getIgnoredPnpmFieldKeys(pnpmConfig.rootProjectManifest)
+      if (ignoredPnpmFieldKeys.length > 0) {
+        warnings.push(`The "pnpm" field in package.json is no longer read by pnpm. The following keys were ignored: ${ignoredPnpmFieldKeys.map(k => `"pnpm.${k}"`).join(', ')}. See https://pnpm.io/settings for the new home of each setting.`)
+      }
       const wantedPmResult = getWantedPackageManager(pnpmConfig.rootProjectManifest)
       if (wantedPmResult.pm) {
         pnpmConfig.wantedPackageManager = wantedPmResult.pm
@@ -750,6 +754,38 @@ function getWantedPackageManager (manifest: ProjectManifest): { pm?: WantedPacka
   return { warnings }
 }
 
+// Settings that used to be read from the `pnpm` field of `package.json` in v10
+// but moved to `pnpm-workspace.yaml` in v11. Keys not in this set (e.g. `app`,
+// or anything set by third-party tooling that piggybacks on the `pnpm` namespace)
+// are left alone to avoid false-positive warnings.
+const MIGRATED_PNPM_FIELD_KEYS = new Set<string>([
+  'allowBuilds',
+  'allowedDeprecatedVersions',
+  'allowUnusedPatches',
+  'auditConfig',
+  'configDependencies',
+  'executionEnv',
+  'ignoredOptionalDependencies',
+  'neverBuiltDependencies',
+  'onlyBuiltDependencies',
+  'onlyBuiltDependenciesFile',
+  'overrides',
+  'packageExtensions',
+  'patchedDependencies',
+  'peerDependencyRules',
+  'requiredScripts',
+  'supportedArchitectures',
+  'updateConfig',
+])
+
+function getIgnoredPnpmFieldKeys (manifest: ProjectManifest): string[] {
+  const legacyField = (manifest as { pnpm?: unknown }).pnpm
+  if (legacyField == null || typeof legacyField !== 'object' || Array.isArray(legacyField)) {
+    return []
+  }
+  return Object.keys(legacyField as Record<string, unknown>).filter(k => MIGRATED_PNPM_FIELD_KEYS.has(k))
+}
+
 export function parsePackageManager (packageManager: string): { name: string, version: string | undefined } {
   if (!packageManager.includes('@')) return { name: packageManager, version: undefined }
   const [name, pmReference] = packageManager.split('@')
diff --git a/config/reader/test/fixtures/pkg-with-legacy-pnpm-field/package.json b/config/reader/test/fixtures/pkg-with-legacy-pnpm-field/package.json
new file mode 100644
index 0000000000..adcad06407
--- /dev/null
+++ b/config/reader/test/fixtures/pkg-with-legacy-pnpm-field/package.json
@@ -0,0 +1,10 @@
+{
+  "pnpm": {
+    "overrides": {
+      "lodash": "^4.17.21"
+    },
+    "patchedDependencies": {
+      "is-odd": "patches/is-odd.patch"
+    }
+  }
+}
diff --git a/config/reader/test/fixtures/pkg-with-pnpm-app-field/package.json b/config/reader/test/fixtures/pkg-with-pnpm-app-field/package.json
new file mode 100644
index 0000000000..9cfaa842a7
--- /dev/null
+++ b/config/reader/test/fixtures/pkg-with-pnpm-app-field/package.json
@@ -0,0 +1,7 @@
+{
+  "pnpm": {
+    "app": {
+      "entry": "dist/index.js"
+    }
+  }
+}
diff --git a/config/reader/test/fixtures/pkg-with-unknown-pnpm-field/package.json b/config/reader/test/fixtures/pkg-with-unknown-pnpm-field/package.json
new file mode 100644
index 0000000000..3e90c1aada
--- /dev/null
+++ b/config/reader/test/fixtures/pkg-with-unknown-pnpm-field/package.json
@@ -0,0 +1,5 @@
+{
+  "pnpm": {
+    "foo": "bar"
+  }
+}
diff --git a/config/reader/test/index.ts b/config/reader/test/index.ts
index cee7de949f..a4403fc924 100644
--- a/config/reader/test/index.ts
+++ b/config/reader/test/index.ts
@@ -1668,6 +1668,47 @@ test('do not return a warning if a package.json has workspaces field and there i
   expect(warnings).toStrictEqual([])
 })
 
+test('return a warning if a package.json has a legacy "pnpm" field with ignored settings', async () => {
+  const prefix = f.find('pkg-with-legacy-pnpm-field')
+  const { warnings } = await getConfig({
+    cliOptions: { dir: prefix },
+    packageManager: {
+      name: 'pnpm',
+      version: '1.0.0',
+    },
+  })
+
+  expect(warnings).toStrictEqual([
+    'The "pnpm" field in package.json is no longer read by pnpm. The following keys were ignored: "pnpm.overrides", "pnpm.patchedDependencies". See https://pnpm.io/settings for the new home of each setting.',
+  ])
+})
+
+test('do not return a warning if a package.json "pnpm" field only contains keys that are still actively read (e.g. "pnpm.app")', async () => {
+  const prefix = f.find('pkg-with-pnpm-app-field')
+  const { warnings } = await getConfig({
+    cliOptions: { dir: prefix },
+    packageManager: {
+      name: 'pnpm',
+      version: '1.0.0',
+    },
+  })
+
+  expect(warnings).toStrictEqual([])
+})
+
+test('do not return a warning if a package.json "pnpm" field only contains keys unrelated to migrated settings (e.g. set by third-party tooling)', async () => {
+  const prefix = f.find('pkg-with-unknown-pnpm-field')
+  const { warnings } = await getConfig({
+    cliOptions: { dir: prefix },
+    packageManager: {
+      name: 'pnpm',
+      version: '1.0.0',
+    },
+  })
+
+  expect(warnings).toStrictEqual([])
+})
+
 test('read PNPM_HOME defined in environment variables', async () => {
   const oldEnv = process.env
   const homeDir = './specified-dir'