diff --git a/.changeset/weak-pets-share.md b/.changeset/weak-pets-share.md
new file mode 100644
index 0000000000..951c0ffbc4
--- /dev/null
+++ b/.changeset/weak-pets-share.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/hoist": patch
+"pnpm": patch
+---
+
+Hoisting with symlinks should not override external symlinks and directories in the root of node_modules.
diff --git a/config/config/package.json b/config/config/package.json
index 2c1cf00100..5765d9fac0 100644
--- a/config/config/package.json
+++ b/config/config/package.json
@@ -61,7 +61,7 @@
     "@types/is-windows": "^1.0.0",
     "@types/ramda": "0.28.15",
     "@types/which": "^2.0.1",
-    "symlink-dir": "^5.0.1"
+    "symlink-dir": "^5.1.0"
   },
   "funding": "https://opencollective.com/pnpm",
   "exports": {
diff --git a/fs/symlink-dependency/package.json b/fs/symlink-dependency/package.json
index 726189ea2e..29f5e5acf9 100644
--- a/fs/symlink-dependency/package.json
+++ b/fs/symlink-dependency/package.json
@@ -42,7 +42,7 @@
   "dependencies": {
     "@pnpm/core-loggers": "workspace:*",
     "@pnpm/types": "workspace:*",
-    "symlink-dir": "^5.0.1"
+    "symlink-dir": "^5.1.0"
   },
   "funding": "https://opencollective.com/pnpm",
   "exports": {
diff --git a/pkg-manager/core/package.json b/pkg-manager/core/package.json
index d3e8340d32..c3ded1617b 100644
--- a/pkg-manager/core/package.json
+++ b/pkg-manager/core/package.json
@@ -97,7 +97,7 @@
     "read-yaml-file": "^2.1.0",
     "resolve-link-target": "^2.0.0",
     "sinon": "^14.0.2",
-    "symlink-dir": "^5.0.1",
+    "symlink-dir": "^5.1.0",
     "write-json-file": "^4.3.0",
     "write-yaml-file": "^4.2.0"
   },
diff --git a/pkg-manager/core/test/install/hoist.ts b/pkg-manager/core/test/install/hoist.ts
index f9cdef5bdf..671ec55c17 100644
--- a/pkg-manager/core/test/install/hoist.ts
+++ b/pkg-manager/core/test/install/hoist.ts
@@ -13,6 +13,7 @@ import rimraf from '@zkochan/rimraf'
 import resolveLinkTarget from 'resolve-link-target'
 import { WANTED_LOCKFILE } from '@pnpm/constants'
 import { addDistTag } from '@pnpm/registry-mock'
+import symlinkDir from 'symlink-dir'
 import writeYamlFile from 'write-yaml-file'
 import { testDefaults } from '../utils'
 
@@ -50,6 +51,24 @@ test('should hoist dependencies to the root of node_modules when publicHoistPatt
   await project.isExecutable('.bin/mime')
 })
 
+test('public hoist should not override directories that are already in the root of node_modules', async () => {
+  const project = prepareEmpty()
+  fs.mkdirSync('node_modules/debug', { recursive: true })
+  fs.writeFileSync('node_modules/debug/pnpm-test.txt', '')
+  fs.mkdirSync('cookie')
+  fs.writeFileSync('cookie/pnpm-test.txt', '')
+  await symlinkDir('cookie', 'node_modules/cookie')
+
+  await addDependenciesToPackage({},
+    ['express@4.18.2'],
+    await testDefaults({ fastUnpack: false, publicHoistPattern: '*' }))
+
+  await project.has('express')
+  await project.has('debug/pnpm-test.txt')
+  await project.has('cookie/pnpm-test.txt')
+  await project.has('mime')
+})
+
 test('should hoist some dependencies to the root of node_modules when publicHoistPattern is used and others to the virtual store directory', async () => {
   const project = prepareEmpty()
 
diff --git a/pkg-manager/hoist/package.json b/pkg-manager/hoist/package.json
index d6bcd71c46..940b157668 100644
--- a/pkg-manager/hoist/package.json
+++ b/pkg-manager/hoist/package.json
@@ -40,16 +40,19 @@
   },
   "dependencies": {
     "@pnpm/constants": "workspace:*",
+    "@pnpm/core-loggers": "workspace:*",
     "@pnpm/link-bins": "workspace:*",
     "@pnpm/lockfile-types": "workspace:*",
     "@pnpm/lockfile-utils": "workspace:*",
     "@pnpm/lockfile-walker": "workspace:*",
     "@pnpm/matcher": "workspace:*",
-    "@pnpm/symlink-dependency": "workspace:*",
     "@pnpm/types": "workspace:*",
     "@pnpm/util.lex-comparator": "1.0.0",
     "dependency-path": "workspace:*",
-    "ramda": "npm:@pnpm/ramda@0.28.1"
+    "is-subdir": "^1.2.0",
+    "ramda": "npm:@pnpm/ramda@0.28.1",
+    "resolve-link-target": "^2.0.0",
+    "symlink-dir": "^5.1.0"
   },
   "funding": "https://opencollective.com/pnpm",
   "exports": {
diff --git a/pkg-manager/hoist/src/index.ts b/pkg-manager/hoist/src/index.ts
index f3091c3db2..e45c9d6d00 100644
--- a/pkg-manager/hoist/src/index.ts
+++ b/pkg-manager/hoist/src/index.ts
@@ -1,4 +1,6 @@
+import fs from 'fs'
 import path from 'path'
+import { linkLogger } from '@pnpm/core-loggers'
 import { WANTED_LOCKFILE } from '@pnpm/constants'
 import { linkBins, WarnFunction } from '@pnpm/link-bins'
 import {
@@ -8,11 +10,13 @@ import {
 import { lockfileWalker, LockfileWalkerStep } from '@pnpm/lockfile-walker'
 import { logger } from '@pnpm/logger'
 import { createMatcher } from '@pnpm/matcher'
-import { symlinkDependency } from '@pnpm/symlink-dependency'
 import { HoistedDependencies } from '@pnpm/types'
 import { lexCompare } from '@pnpm/util.lex-comparator'
 import * as dp from 'dependency-path'
+import isSubdir from 'is-subdir'
 import mapObjIndexed from 'ramda/src/mapObjIndexed'
+import resolveLinkTarget from 'resolve-link-target'
+import symlinkDir from 'symlink-dir'
 
 const hoistLogger = logger('hoist')
 
@@ -202,6 +206,7 @@ async function symlinkHoistedDependencies (
     virtualStoreDir: string
   }
 ) {
+  const symlink = symlinkHoistedDependency.bind(null, opts)
   await Promise.all(
     Object.entries(hoistedDependencies)
       .map(async ([depPath, pkgAliases]) => {
@@ -218,8 +223,44 @@ async function symlinkHoistedDependencies (
           const targetDir = hoistType === 'public'
             ? opts.publicHoistedModulesDir
             : opts.privateHoistedModulesDir
-          await symlinkDependency(depLocation, targetDir, pkgAlias)
+          const dest = path.join(targetDir, pkgAlias)
+          return symlink(depLocation, dest)
         }))
-      }
-      ))
+      })
+  )
+}
+
+async function symlinkHoistedDependency (
+  opts: { virtualStoreDir: string },
+  depLocation: string,
+  dest: string
+) {
+  try {
+    await symlinkDir(depLocation, dest, { overwrite: false })
+    linkLogger.debug({ target: dest, link: depLocation })
+    return
+  } catch (err: any) { // eslint-disable-line
+    if (err.code !== 'EEXIST' && err.code !== 'EISDIR') throw err
+  }
+  let existingSymlink!: string
+  try {
+    existingSymlink = await resolveLinkTarget(dest)
+  } catch (err) {
+    hoistLogger.debug({
+      skipped: dest,
+      reason: 'a directory is present at the target location',
+    })
+    return
+  }
+  if (!isSubdir(opts.virtualStoreDir, existingSymlink)) {
+    hoistLogger.debug({
+      skipped: dest,
+      existingSymlink,
+      reason: 'an external symlink is present at the target location',
+    })
+    return
+  }
+  await fs.promises.unlink(dest)
+  await symlinkDir(depLocation, dest)
+  linkLogger.debug({ target: dest, link: depLocation })
 }
diff --git a/pkg-manager/hoist/tsconfig.json b/pkg-manager/hoist/tsconfig.json
index fbe1f3e514..9d72521ae2 100644
--- a/pkg-manager/hoist/tsconfig.json
+++ b/pkg-manager/hoist/tsconfig.json
@@ -12,9 +12,6 @@
     {
       "path": "../../config/matcher"
     },
-    {
-      "path": "../../fs/symlink-dependency"
-    },
     {
       "path": "../../lockfile/lockfile-types"
     },
@@ -27,6 +24,9 @@
     {
       "path": "../../packages/constants"
     },
+    {
+      "path": "../../packages/core-loggers"
+    },
     {
       "path": "../../packages/dependency-path"
     },
diff --git a/pkg-manager/link-bins/package.json b/pkg-manager/link-bins/package.json
index 518e57db27..26291262e9 100644
--- a/pkg-manager/link-bins/package.json
+++ b/pkg-manager/link-bins/package.json
@@ -46,7 +46,7 @@
     "normalize-path": "^3.0.0",
     "p-settle": "^4.1.1",
     "ramda": "npm:@pnpm/ramda@0.28.1",
-    "symlink-dir": "^5.0.1"
+    "symlink-dir": "^5.1.0"
   },
   "devDependencies": {
     "@pnpm/link-bins": "workspace:*",
diff --git a/pkg-manager/plugin-commands-installation/package.json b/pkg-manager/plugin-commands-installation/package.json
index 9ca9af5471..5f1691b6c8 100644
--- a/pkg-manager/plugin-commands-installation/package.json
+++ b/pkg-manager/plugin-commands-installation/package.json
@@ -51,7 +51,7 @@
     "proxyquire": "^2.1.3",
     "read-yaml-file": "^2.1.0",
     "sinon": "^14.0.2",
-    "symlink-dir": "^5.0.1",
+    "symlink-dir": "^5.1.0",
     "tempy": "^1.0.1",
     "write-json-file": "^4.3.0",
     "write-pkg": "4.0.0",
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 78c9f0957d..f9638dfae1 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -607,8 +607,8 @@ importers:
         specifier: ^2.0.1
         version: 2.0.1
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
 
   config/matcher:
     dependencies:
@@ -1466,8 +1466,8 @@ importers:
         specifier: workspace:*
         version: link:../../packages/types
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
     devDependencies:
       '@pnpm/prepare':
         specifier: workspace:*
@@ -2703,8 +2703,8 @@ importers:
         specifier: ^14.0.2
         version: 14.0.2
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
       write-json-file:
         specifier: ^4.3.0
         version: 4.3.0
@@ -2920,6 +2920,9 @@ importers:
       '@pnpm/constants':
         specifier: workspace:*
         version: link:../../packages/constants
+      '@pnpm/core-loggers':
+        specifier: workspace:*
+        version: link:../../packages/core-loggers
       '@pnpm/link-bins':
         specifier: workspace:*
         version: link:../link-bins
@@ -2938,9 +2941,6 @@ importers:
       '@pnpm/matcher':
         specifier: workspace:*
         version: link:../../config/matcher
-      '@pnpm/symlink-dependency':
-        specifier: workspace:*
-        version: link:../../fs/symlink-dependency
       '@pnpm/types':
         specifier: workspace:*
         version: link:../../packages/types
@@ -2950,9 +2950,18 @@ importers:
       dependency-path:
         specifier: workspace:*
         version: link:../../packages/dependency-path
+      is-subdir:
+        specifier: ^1.2.0
+        version: 1.2.0
       ramda:
         specifier: npm:@pnpm/ramda@0.28.1
         version: /@pnpm/ramda/0.28.1
+      resolve-link-target:
+        specifier: ^2.0.0
+        version: 2.0.0
+      symlink-dir:
+        specifier: ^5.1.0
+        version: 5.1.0
     devDependencies:
       '@pnpm/hoist':
         specifier: workspace:*
@@ -3012,8 +3021,8 @@ importers:
         specifier: npm:@pnpm/ramda@0.28.1
         version: /@pnpm/ramda/0.28.1
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
     devDependencies:
       '@pnpm/link-bins':
         specifier: workspace:*
@@ -3453,8 +3462,8 @@ importers:
         specifier: ^14.0.2
         version: 14.0.2
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
       tempy:
         specifier: ^1.0.1
         version: 1.0.1
@@ -4060,8 +4069,8 @@ importers:
         specifier: ^6.0.1
         version: 6.0.1
       symlink-dir:
-        specifier: ^5.0.1
-        version: 5.0.1
+        specifier: ^5.1.0
+        version: 5.1.0
       tempy:
         specifier: ^1.0.1
         version: 1.0.1
@@ -16115,6 +16124,15 @@ packages:
     dependencies:
       better-path-resolve: 1.0.0
       rename-overwrite: 4.0.3
+    dev: true
+
+  /symlink-dir/5.1.0:
+    resolution: {integrity: sha512-nrwSDbmMYGwc+wu6gzmTdQIV9GzItMG/0LX4c9Co0bhtx2KK1WUKjNIyhjhAdIKaA5eIwVhB2tqFsn8ooUsRKA==}
+    engines: {node: '>=12.10'}
+    hasBin: true
+    dependencies:
+      better-path-resolve: 1.0.0
+      rename-overwrite: 4.0.3
 
   /syncpack/8.3.9:
     resolution: {integrity: sha512-oDaEvgZAoU40WXX4okQ7DiCfVEcO2antl+jV+Av+FbS4Hyh8VoJ8F6HGo2G8eT9H+AyBBM1iDUdbtR1MQRimoQ==}
@@ -17529,7 +17547,7 @@ time:
   /string.prototype.replaceall/1.0.6: '2021-10-05T01:00:00.092Z'
   /strip-ansi/6.0.1: '2021-09-23T16:34:41.798Z'
   /strip-bom/4.0.0: '2019-04-28T04:40:47.887Z'
-  /symlink-dir/5.0.1: '2021-05-03T15:54:10.299Z'
+  /symlink-dir/5.1.0: '2022-11-20T16:48:15.918Z'
   /syncpack/8.3.9: '2022-10-28T16:58:42.312Z'
   /tar-stream/2.2.0: '2020-12-29T10:22:57.508Z'
   /tar/6.1.12: '2022-11-01T16:33:12.294Z'
diff --git a/pnpm/package.json b/pnpm/package.json
index e310c56cb4..f20f7a5a9b 100644
--- a/pnpm/package.json
+++ b/pnpm/package.json
@@ -101,7 +101,7 @@
     "semver": "^7.3.8",
     "split-cmd": "^1.0.1",
     "strip-ansi": "^6.0.1",
-    "symlink-dir": "^5.0.1",
+    "symlink-dir": "^5.1.0",
     "tempy": "^1.0.1",
     "tree-kill": "^1.2.2",
     "which": "^2.0.2",