diff --git a/.changeset/fix-global-bin-subdir.md b/.changeset/fix-global-bin-subdir.md
new file mode 100644
index 0000000000..f06dbc09aa
--- /dev/null
+++ b/.changeset/fix-global-bin-subdir.md
@@ -0,0 +1,9 @@
+---
+"@pnpm/config.reader": minor
+"@pnpm/engine.pm.commands": minor
+"pnpm": minor
+---
+
+Store globally installed binaries in a `bin` subdirectory of `PNPM_HOME` instead of directly in `PNPM_HOME`. This prevents internal directories like `global/` and `store/` from polluting shell autocompletion when `PNPM_HOME` is on PATH [#10986](https://github.com/pnpm/pnpm/issues/10986).
+
+After upgrading, run `pnpm setup` to update your shell configuration.
diff --git a/config/reader/src/checkGlobalBinDir.ts b/config/reader/src/checkGlobalBinDir.ts
index 289540dc98..63ca5b9d74 100644
--- a/config/reader/src/checkGlobalBinDir.ts
+++ b/config/reader/src/checkGlobalBinDir.ts
@@ -15,10 +15,12 @@ export async function checkGlobalBinDir (
       `Couldn't find a global directory for executables because the "${PATH}" environment variable is not set.`)
   }
   if (!await globalBinDirIsInPath(globalBinDir, env)) {
-    throw new PnpmError('GLOBAL_BIN_DIR_NOT_IN_PATH', `The configured global bin directory "${globalBinDir}" is not in PATH`)
+    throw new PnpmError('GLOBAL_BIN_DIR_NOT_IN_PATH', `The configured global bin directory "${globalBinDir}" is not in PATH`, {
+      hint: 'Run "pnpm setup" to update your shell configuration.',
+    })
   }
   if (shouldAllowWrite && !canWriteToDirAndExists(globalBinDir)) {
-    throw new PnpmError('PNPM_DIR_NOT_WRITABLE', `The CLI has no write access to the pnpm home directory at ${globalBinDir}`)
+    throw new PnpmError('PNPM_DIR_NOT_WRITABLE', `The CLI has no write access to the global bin directory at ${globalBinDir}`)
   }
 }
 
diff --git a/config/reader/src/index.ts b/config/reader/src/index.ts
index 5f1e71cf16..6cf9e8da58 100644
--- a/config/reader/src/index.ts
+++ b/config/reader/src/index.ts
@@ -324,7 +324,7 @@ export async function getConfig (opts: {
   pnpmConfig.authInfos = networkConfigs.authInfos ?? {} // TODO: remove `?? {}` (when possible)
   pnpmConfig.sslConfigs = networkConfigs.sslConfigs
   Object.assign(pnpmConfig, getDefaultAuthInfo(pnpmConfig.rawConfig))
-  pnpmConfig.pnpmHomeDir = getDataDir(process)
+  pnpmConfig.pnpmHomeDir = getDataDir({ env, platform: process.platform })
   let globalDirRoot
   if (pnpmConfig.globalDir) {
     globalDirRoot = pnpmConfig.globalDir
@@ -335,7 +335,7 @@ export async function getConfig (opts: {
   pnpmConfig.dir = cwd
   if (cliOptions['global']) {
     delete pnpmConfig.workspaceDir
-    pnpmConfig.bin = npmConfig.get('global-bin-dir') ?? env.PNPM_HOME
+    pnpmConfig.bin = npmConfig.get('global-bin-dir') ?? path.join(pnpmConfig.pnpmHomeDir, 'bin')
     if (pnpmConfig.bin) {
       fs.mkdirSync(pnpmConfig.bin, { recursive: true })
       await checkGlobalBinDir(pnpmConfig.bin, { env, shouldAllowWrite: opts.globalDirShouldAllowWrite })
diff --git a/config/reader/test/index.ts b/config/reader/test/index.ts
index d57656696d..6ea942e283 100644
--- a/config/reader/test/index.ts
+++ b/config/reader/test/index.ts
@@ -34,7 +34,7 @@ for (const suffix of [
 
 const env = {
   PNPM_HOME: import.meta.dirname,
-  [PATH]: import.meta.dirname,
+  [PATH]: path.join(import.meta.dirname, 'bin'),
 }
 const f = fixtures(import.meta.dirname)
 
diff --git a/engine/pm/commands/src/self-updater/selfUpdate.ts b/engine/pm/commands/src/self-updater/selfUpdate.ts
index 02335fdb91..fdad55da13 100644
--- a/engine/pm/commands/src/self-updater/selfUpdate.ts
+++ b/engine/pm/commands/src/self-updater/selfUpdate.ts
@@ -132,8 +132,8 @@ export async function handler (
     storeDir: store.dir,
   })
 
-  // Link bins to pnpmHomeDir so the updated pnpm is the active global binary
-  await linkBins(path.join(baseDir, 'node_modules'), opts.pnpmHomeDir, { warn: globalWarn })
+  // Link bins to pnpmHomeDir/bin so the updated pnpm is the active global binary
+  await linkBins(path.join(baseDir, 'node_modules'), path.join(opts.pnpmHomeDir, 'bin'), { warn: globalWarn })
 
   if (alreadyExisted) {
     return `The ${bareSpecifier} version, v${resolution.manifest.version}, is already present on the system. It was activated by linking it from ${baseDir}.`
diff --git a/engine/pm/commands/src/setup/setup.ts b/engine/pm/commands/src/setup/setup.ts
index 6c26d88635..24ce0b5c30 100644
--- a/engine/pm/commands/src/setup/setup.ts
+++ b/engine/pm/commands/src/setup/setup.ts
@@ -135,14 +135,16 @@ export async function handler (
   }
 ): Promise<string> {
   const execPath = getExecPath()
+  const binDir = path.join(opts.pnpmHomeDir, 'bin')
   if (execPath.match(/\.[cm]?js$/) == null) {
     installCliGlobally(execPath, opts.pnpmHomeDir)
-    createPnpxScripts(opts.pnpmHomeDir)
+    createPnpxScripts(binDir)
   }
   try {
     const report = await addDirToEnvPath(opts.pnpmHomeDir, {
       configSectionName: 'pnpm',
       proxyVarName: 'PNPM_HOME',
+      proxyVarSubDir: 'bin',
       overwrite: opts.force,
       position: 'start',
     })
diff --git a/engine/pm/commands/test/self-updater/selfUpdate.test.ts b/engine/pm/commands/test/self-updater/selfUpdate.test.ts
index cf0c04ec66..c61d6ef281 100644
--- a/engine/pm/commands/test/self-updater/selfUpdate.test.ts
+++ b/engine/pm/commands/test/self-updater/selfUpdate.test.ts
@@ -56,7 +56,7 @@ function prepareOptions (dir: string) {
     rawLocalConfig: {},
     sort: false,
     rootProjectManifestDir: dir,
-    bin: dir,
+    bin: path.join(dir, 'bin'),
     workspaceConcurrency: 1,
     extraEnv: {},
     pnpmfile: '',
@@ -147,7 +147,7 @@ test('self-update', async () => {
   const pnpmPkgJson = JSON.parse(fs.readFileSync(path.join(globalDir, installDirName!, 'node_modules/pnpm/package.json'), 'utf8'))
   expect(pnpmPkgJson.version).toBe('9.1.0')
 
-  const pnpmEnv = prependDirsToPath([opts.pnpmHomeDir])
+  const pnpmEnv = prependDirsToPath([path.join(opts.pnpmHomeDir, 'bin')])
   const { status, stdout } = spawn.sync('pnpm', ['-v'], {
     env: {
       ...process.env,
@@ -180,7 +180,7 @@ test('self-update by exact version', async () => {
   const pnpmPkgJson = JSON.parse(fs.readFileSync(path.join(globalDir, installDirName!, 'node_modules/pnpm/package.json'), 'utf8'))
   expect(pnpmPkgJson.version).toBe('9.1.0')
 
-  const pnpmEnv = prependDirsToPath([opts.pnpmHomeDir])
+  const pnpmEnv = prependDirsToPath([path.join(opts.pnpmHomeDir, 'bin')])
   const { status, stdout } = spawn.sync('pnpm', ['-v'], {
     env: {
       ...process.env,
@@ -418,7 +418,7 @@ console.log('9.2.0')`, 'utf8')
 
   expect(output).toBe(`The latest version, v9.2.0, is already present on the system. It was activated by linking it from ${installDir}.`)
 
-  const pnpmEnv = prependDirsToPath([opts.pnpmHomeDir])
+  const pnpmEnv = prependDirsToPath([path.join(opts.pnpmHomeDir, 'bin')])
   const { status, stdout } = spawn.sync('pnpm', ['-v'], {
     env: {
       ...process.env,
@@ -438,7 +438,7 @@ test('self-update works globally without package.json', async () => {
     ...prepareOptions(dir),
     globalPkgDir: path.join(pnpmHomeDir, 'global', 'v11'),
     pnpmHomeDir,
-    bin: pnpmHomeDir,
+    bin: path.join(pnpmHomeDir, 'bin'),
   }
   mockRegistryForUpdate(opts.registries.default, '9.1.0', createMetadata('9.1.0', opts.registries.default))
 
@@ -457,7 +457,7 @@ test('self-update works globally without package.json', async () => {
   expect(globalInstallDir).toBeDefined()
   expect(fs.existsSync(path.join(globalDir, globalInstallDir!, 'node_modules', 'pnpm', 'package.json'))).toBe(true)
 
-  const pnpmEnv = prependDirsToPath([pnpmHomeDir])
+  const pnpmEnv = prependDirsToPath([path.join(pnpmHomeDir, 'bin')])
   const { status, stdout } = spawn.sync('pnpm', ['-v'], {
     env: {
       ...process.env,
diff --git a/engine/runtime/commands/src/env/utils.ts b/engine/runtime/commands/src/env/utils.ts
index 43983ce2de..fa2ea7d41e 100644
--- a/engine/runtime/commands/src/env/utils.ts
+++ b/engine/runtime/commands/src/env/utils.ts
@@ -1,7 +1,7 @@
 import path from 'node:path'
 
 export function getNodeExecPathInBinDir (pnpmHomeDir: string): string {
-  return path.resolve(pnpmHomeDir, process.platform === 'win32' ? 'node.exe' : 'node')
+  return path.resolve(pnpmHomeDir, 'bin', process.platform === 'win32' ? 'node.exe' : 'node')
 }
 
 export function getNodeExecPathInNodeDir (nodeDir: string): string {
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 118292f73b..73ae2d9afa 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -257,8 +257,8 @@ catalogs:
       specifier: ^2.0.0
       version: 2.0.0
     '@pnpm/os.env.path-extender':
-      specifier: ^2.0.3
-      version: 2.0.3
+      specifier: ^3.0.0
+      version: 3.0.0
     '@pnpm/patch-package':
       specifier: 0.0.1
       version: 0.0.1
@@ -3499,7 +3499,7 @@ importers:
         version: link:../../../lockfile/types
       '@pnpm/os.env.path-extender':
         specifier: 'catalog:'
-        version: 2.0.3
+        version: 3.0.0
       '@pnpm/resolving.npm-resolver':
         specifier: workspace:*
         version: link:../../../resolving/npm-resolver
@@ -10528,17 +10528,17 @@ packages:
     resolution: {integrity: sha512-YTJCXyUGOrJuj4QqhSKqZa1vlVAm82h1/uw00ZmD/kL2OViggtyUwWyIe62kpwWVPwEYixfGjfvaFKVJy2mjzA==}
     engines: {node: '>=18.12'}
 
-  '@pnpm/os.env.path-extender-posix@2.1.0':
-    resolution: {integrity: sha512-oE0WCU2GCdOS/ChBi0dAFkktpxe0EPvCswP6+15yaHuydrCBTAaoB9cqSQaQCYrrDbabhn3kSxTex2T5xhq9fg==}
-    engines: {node: '>=18.12'}
+  '@pnpm/os.env.path-extender-posix@3.0.0':
+    resolution: {integrity: sha512-541CmvX6CPc/YkLPEiqxXRj9dEd4Bd/LVeL4WZ4WZQaK/R/Rld2pxljoEHtx6bI91z2p+esG2OFOvnaHVyYr2A==}
+    engines: {node: '>=22.13'}
 
-  '@pnpm/os.env.path-extender-windows@2.0.3':
-    resolution: {integrity: sha512-zJlGIoRLNpZh9xhCgC6nTvqvXzw1wKhiH3TuroJQ0xHxDwVxk7kAbF4wSROBcVcdOnK4zlxsA1Vc0jAPjxInog==}
-    engines: {node: '>=18.12'}
+  '@pnpm/os.env.path-extender-windows@3.0.0':
+    resolution: {integrity: sha512-P2z4D6TnCTfe0CL+p2lgtkOovbJbmb4t5xf1GJ/s3Lptf68HGhqbY5E3z1tg7vT9Hs4WN8kL6fbS+0378VOdYw==}
+    engines: {node: '>=22.13'}
 
-  '@pnpm/os.env.path-extender@2.0.3':
-    resolution: {integrity: sha512-Tnrcwi0kGBaMPT9amiWg2ANbdIWMxVJS/d62lNMHbWX3erY2MAG9Y7Si46qdshrYlOzeqHX/lrW5AjlgF/zNeQ==}
-    engines: {node: '>=18.12'}
+  '@pnpm/os.env.path-extender@3.0.0':
+    resolution: {integrity: sha512-gNA3d1w8m7JlyXfjurpqZ+SwWq91JVhrUcsNIGh64r/4Nxnq3o+yxUQyxyrBFlL8luW6OcL0cFfYdAkv19n78Q==}
+    engines: {node: '>=22.13'}
 
   '@pnpm/package-bins@1000.0.17':
     resolution: {integrity: sha512-DD2XTIIWwN1xVRdocKRaIl4eSMp3EdhhxqogfEwEiMbmGkoE4lbnTg3f81VEfhOGl1vTaS5UoM2qxW1FGrpaZQ==}
@@ -18489,20 +18489,21 @@ snapshots:
       '@pnpm/util.lex-comparator': 3.0.2
       sort-keys: 4.2.0
 
-  '@pnpm/os.env.path-extender-posix@2.1.0':
+  '@pnpm/os.env.path-extender-posix@3.0.0':
     dependencies:
       '@pnpm/error': 1000.0.5
 
-  '@pnpm/os.env.path-extender-windows@2.0.3':
+  '@pnpm/os.env.path-extender-windows@3.0.0':
     dependencies:
       '@pnpm/error': 1000.0.5
       safe-execa: 0.1.4
       string.prototype.matchall: 4.0.12
 
-  '@pnpm/os.env.path-extender@2.0.3':
+  '@pnpm/os.env.path-extender@3.0.0':
     dependencies:
-      '@pnpm/os.env.path-extender-posix': 2.1.0
-      '@pnpm/os.env.path-extender-windows': 2.0.3
+      '@pnpm/error': 1000.0.5
+      '@pnpm/os.env.path-extender-posix': 3.0.0
+      '@pnpm/os.env.path-extender-windows': 3.0.0
 
   '@pnpm/package-bins@1000.0.17':
     dependencies:
diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml
index 26945f0d31..8c644aaa29 100644
--- a/pnpm-workspace.yaml
+++ b/pnpm-workspace.yaml
@@ -90,7 +90,7 @@ catalog:
   '@pnpm/npm-conf': 3.0.2
   '@pnpm/npm-lifecycle': ^1001.0.0
   '@pnpm/npm-package-arg': ^2.0.0
-  '@pnpm/os.env.path-extender': ^2.0.3
+  '@pnpm/os.env.path-extender': ^3.0.0
   '@pnpm/patch-package': 0.0.1
   '@pnpm/registry-mock': 5.2.4
   '@pnpm/semver-diff': ^1.1.0
diff --git a/pnpm/test/bin.ts b/pnpm/test/bin.ts
index b143b381cc..9a7d41b54a 100644
--- a/pnpm/test/bin.ts
+++ b/pnpm/test/bin.ts
@@ -19,13 +19,14 @@ test('pnpm bin', async () => {
 test('pnpm bin -g', async () => {
   tempDir()
 
+  const binDir = path.join(process.cwd(), 'bin')
   const env = {
     PNPM_HOME: process.cwd(),
-    [PATH_NAME]: process.cwd(),
+    [PATH_NAME]: binDir,
   }
 
   const result = execPnpmSync(['bin', '-g'], { env })
 
   expect(result.status).toBe(0)
-  expect(result.stdout.toString().trim()).toEqual(env.PNPM_HOME)
+  expect(result.stdout.toString().trim()).toEqual(binDir)
 })
diff --git a/pnpm/test/install/global.ts b/pnpm/test/install/global.ts
index 91012b7dbb..7117fdfcdb 100644
--- a/pnpm/test/install/global.ts
+++ b/pnpm/test/install/global.ts
@@ -57,7 +57,7 @@ test('global installation', async () => {
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   await execPnpm(['add', '--global', 'is-positive'], { env })
 
@@ -87,7 +87,7 @@ test('global install warns when project has packageManager configured', async ()
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   const { status } = execPnpmSync([
     'add',
@@ -103,7 +103,7 @@ test('global installation to custom directory with --global-dir', async () => {
   prepare()
   const global = path.resolve('..', 'global')
   const pnpmHome = path.join(global, 'pnpm')
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome }
 
   await execPnpm(['add', '--global', '--global-dir=../global', 'is-positive'], { env })
 
@@ -121,7 +121,7 @@ test('always install latest when doing global installation without spec', async
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   await execPnpm(['add', '-g', '@pnpm.e2e/peer-c@1'], { env })
   await execPnpm(['add', '-g', '@pnpm.e2e/peer-c'], { env })
@@ -143,7 +143,7 @@ test('run lifecycle events of global packages in correct working directory', asy
   fs.mkdirSync(pnpmHome, { recursive: true })
 
   const env = {
-    [PATH_NAME]: `${pnpmHome}${path.delimiter}${process.env[PATH_NAME]!}`,
+    [PATH_NAME]: `${path.join(pnpmHome, 'bin')}${path.delimiter}${process.env[PATH_NAME]!}`,
     PNPM_HOME: pnpmHome,
     XDG_DATA_HOME: global,
   }
@@ -188,7 +188,7 @@ test.skip('dangerously-allow-all-builds=true in global config', async () => {
   ].join('\n'))
 
   const env = {
-    [PATH_NAME]: `${pnpmHome}${path.delimiter}${process.env[PATH_NAME]!}`,
+    [PATH_NAME]: `${path.join(pnpmHome, 'bin')}${path.delimiter}${process.env[PATH_NAME]!}`,
     HOME: home,
     XDG_CONFIG_HOME: cfgHome,
     PNPM_HOME: pnpmHome,
@@ -246,7 +246,7 @@ test.skip('dangerously-allow-all-builds=false in global config', async () => {
   ].join('\n'))
 
   const env = {
-    [PATH_NAME]: `${pnpmHome}${path.delimiter}${process.env[PATH_NAME]!}`,
+    [PATH_NAME]: `${path.join(pnpmHome, 'bin')}${path.delimiter}${process.env[PATH_NAME]!}`,
     HOME: home,
     XDG_CONFIG_HOME: cfgHome,
     PNPM_HOME: pnpmHome,
@@ -277,7 +277,7 @@ test('global update to latest', async () => {
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   await execPnpm(['add', '--global', 'is-positive@1'], { env })
   await execPnpm(['update', '--global', '--latest'], { env })
@@ -294,7 +294,7 @@ test('global update should not crash if there are no global packages', async ()
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   expect(execPnpmSync(['update', '--global'], { env }).status).toBe(0)
 })
@@ -305,7 +305,7 @@ test('global add cleans up stale bins when re-adding a package with different bi
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(pnpmHome, { recursive: true })
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   // Create v1 tarball with bin "old-bin"
   const pkgDir = path.resolve('..', 'my-tool')
@@ -320,7 +320,7 @@ test('global add cleans up stale bins when re-adding a package with different bi
   execPnpmSync(['pack', '--pack-destination', pkgDir], { cwd: path.join(pkgDir, 'package') })
 
   await execPnpm(['add', '-g', tarballV1], { env })
-  expect(fs.existsSync(path.join(pnpmHome, 'old-bin'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'old-bin'))).toBeTruthy()
 
   // Create v2 tarball with bin "new-bin"
   fs.writeFileSync(path.join(pkgDir, 'package', 'package.json'), JSON.stringify({
@@ -335,8 +335,8 @@ test('global add cleans up stale bins when re-adding a package with different bi
   await execPnpm(['add', '-g', tarballV2], { env })
 
   // old-bin should be gone, new-bin should exist
-  expect(fs.existsSync(path.join(pnpmHome, 'old-bin'))).toBeFalsy()
-  expect(fs.existsSync(path.join(pnpmHome, 'new-bin'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'old-bin'))).toBeFalsy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'new-bin'))).toBeTruthy()
 })
 
 test('global add refuses to install when bin name conflicts with another global package', async () => {
@@ -345,7 +345,7 @@ test('global add refuses to install when bin name conflicts with another global
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(pnpmHome, { recursive: true })
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   // Create two local packages that both expose a bin called "my-bin"
   const pkgA = path.resolve('..', 'pkg-a')
@@ -395,8 +395,9 @@ test('global add from a local directory using "."', () => {
   }))
   fs.writeFileSync(path.join(localPkg, 'index.js'), '#!/usr/bin/env node\nconsole.log("hello")\n')
 
+  const globalBin = path.join(pnpmHome, 'bin')
   const env = {
-    [PATH_NAME]: pnpmHome,
+    [PATH_NAME]: globalBin,
     PNPM_HOME: pnpmHome,
     XDG_DATA_HOME: global,
     pnpm_config_store_dir: path.resolve('..', 'store'),
@@ -411,17 +412,17 @@ test('global add from a local directory using "."', () => {
   expect(findGlobalPkg(globalPkgDir(pnpmHome), 'my-local-tool')).toBeTruthy()
 
   // Verify the bin was linked
-  expect(fs.existsSync(path.join(pnpmHome, 'my-local-tool'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'my-local-tool'))).toBeTruthy()
 
   // Install globally using a file: relative selector
   execPnpmSync(['add', '-g', 'file:./'], { cwd: localPkg, env, expectSuccess: true })
   expect(findGlobalPkg(globalPkgDir(pnpmHome), 'my-local-tool')).toBeTruthy()
-  expect(fs.existsSync(path.join(pnpmHome, 'my-local-tool'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'my-local-tool'))).toBeTruthy()
 
   // Install globally using a link: relative selector
   execPnpmSync(['add', '-g', 'link:../my-local-tool'], { cwd: process.cwd(), env, expectSuccess: true })
   expect(findGlobalPkg(globalPkgDir(pnpmHome), 'my-local-tool')).toBeTruthy()
-  expect(fs.existsSync(path.join(pnpmHome, 'my-local-tool'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'my-local-tool'))).toBeTruthy()
 })
 
 test('global remove deletes install group and bin shims', async () => {
@@ -430,7 +431,7 @@ test('global remove deletes install group and bin shims', async () => {
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(pnpmHome, { recursive: true })
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   // Create two packages with bins and install them together as a group
   const pkgA = path.resolve('..', 'tool-a')
@@ -453,13 +454,13 @@ test('global remove deletes install group and bin shims', async () => {
 
   // Install as a group
   await execPnpm(['add', '-g', pkgA, pkgB], { env })
-  expect(fs.existsSync(path.join(pnpmHome, 'tool-a-bin'))).toBeTruthy()
-  expect(fs.existsSync(path.join(pnpmHome, 'tool-b-bin'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'tool-a-bin'))).toBeTruthy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'tool-b-bin'))).toBeTruthy()
 
   // Remove one package — entire group (both bins) should be removed
   await execPnpm(['remove', '-g', 'tool-a'], { env })
-  expect(fs.existsSync(path.join(pnpmHome, 'tool-a-bin'))).toBeFalsy()
-  expect(fs.existsSync(path.join(pnpmHome, 'tool-b-bin'))).toBeFalsy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'tool-a-bin'))).toBeFalsy()
+  expect(fs.existsSync(path.join(pnpmHome, 'bin', 'tool-b-bin'))).toBeFalsy()
   expect(findGlobalPkg(globalPkgDir(pnpmHome), 'tool-a')).toBeNull()
   expect(findGlobalPkg(globalPkgDir(pnpmHome), 'tool-b')).toBeNull()
 })
diff --git a/pnpm/test/root.ts b/pnpm/test/root.ts
index f3ee5d7949..73ddd9c47f 100644
--- a/pnpm/test/root.ts
+++ b/pnpm/test/root.ts
@@ -25,7 +25,7 @@ test('pnpm root -g', async () => {
   const pnpmHome = path.join(global, 'pnpm')
   fs.mkdirSync(global)
 
-  const env = { [PATH_NAME]: pnpmHome, PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
+  const env = { [PATH_NAME]: path.join(pnpmHome, 'bin'), PNPM_HOME: pnpmHome, XDG_DATA_HOME: global }
 
   const result = execPnpmSync(['root', '-g'], { env })
 
diff --git a/pnpm/test/uninstall.ts b/pnpm/test/uninstall.ts
index b31ec0143f..ce6e72fa0a 100644
--- a/pnpm/test/uninstall.ts
+++ b/pnpm/test/uninstall.ts
@@ -31,10 +31,11 @@ test('uninstall global package with its bin files', async () => {
   prepare()
 
   const global = process.cwd()
-  const globalBin = path.resolve(global, 'bin')
+  const pnpmHome = path.resolve(global, 'pnpm')
+  const globalBin = path.join(pnpmHome, 'bin')
 
   const env = {
-    PNPM_HOME: globalBin,
+    PNPM_HOME: pnpmHome,
     [PATH]: `${globalBin}${path.delimiter}${process.env[PATH] ?? ''}`,
     XDG_DATA_HOME: global,
   }