diff --git a/.changeset/happy-paws-walk.md b/.changeset/happy-paws-walk.md
new file mode 100644
index 0000000000..809dbae153
--- /dev/null
+++ b/.changeset/happy-paws-walk.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-script-runners": patch
+"pnpm": patch
+---
+
+When running "pnpm exec" from a subdirectory of a project, don't change the current working directory to the root of the project [#5759](https://github.com/pnpm/pnpm/issues/5759).
diff --git a/exec/plugin-commands-script-runners/src/exec.ts b/exec/plugin-commands-script-runners/src/exec.ts
index 20df4608ca..7658290638 100644
--- a/exec/plugin-commands-script-runners/src/exec.ts
+++ b/exec/plugin-commands-script-runners/src/exec.ts
@@ -146,6 +146,7 @@ export type ExecOpts = Required<Pick<Config, 'selectedProjectsGraph'>> & {
   implicitlyFellbackFromRun?: boolean
 } & Pick<Config,
 | 'bin'
+| 'cliOptions'
 | 'dir'
 | 'extraBinPaths'
 | 'extraEnv'
@@ -187,7 +188,7 @@ export async function handler (
       chunks = chunks.reverse()
     }
   } else {
-    chunks = [[opts.dir as ProjectRootDir]]
+    chunks = [[(opts.cliOptions.dir ?? process.cwd()) as ProjectRootDir]]
     const project = await tryReadProjectManifest(opts.dir)
     if (project.manifest != null) {
       opts.selectedProjectsGraph = {
diff --git a/exec/plugin-commands-script-runners/src/run.ts b/exec/plugin-commands-script-runners/src/run.ts
index 5838254437..1e5c7717c9 100644
--- a/exec/plugin-commands-script-runners/src/run.ts
+++ b/exec/plugin-commands-script-runners/src/run.ts
@@ -158,6 +158,7 @@ export type RunOpts =
   & { recursive?: boolean }
   & Pick<Config,
   | 'bin'
+  | 'cliOptions'
   | 'verifyDepsBeforeRun'
   | 'dir'
   | 'enablePrePostScripts'
diff --git a/exec/plugin-commands-script-runners/test/exec.e2e.ts b/exec/plugin-commands-script-runners/test/exec.e2e.ts
index 23e6ca8f36..ba9b600cbd 100644
--- a/exec/plugin-commands-script-runners/test/exec.e2e.ts
+++ b/exec/plugin-commands-script-runners/test/exec.e2e.ts
@@ -157,6 +157,7 @@ test('exec inside a workspace package', async () => {
     '--store-dir',
     path.resolve(DEFAULT_OPTS.storeDir),
   ])
+  process.chdir('project-1')
   await exec.handler({
     ...DEFAULT_OPTS,
     dir: path.resolve('project-1'),
diff --git a/pnpm/test/exec.ts b/pnpm/test/exec.ts
new file mode 100644
index 0000000000..87d40f146b
--- /dev/null
+++ b/pnpm/test/exec.ts
@@ -0,0 +1,29 @@
+import fs from 'fs'
+import path from 'path'
+import { prepare } from '@pnpm/prepare'
+import { execPnpm, execPnpmSync } from './utils/index.js'
+
+test("exec should respect the caller's current working directory", async () => {
+  prepare({
+    name: 'root',
+    version: '1.0.0',
+  })
+
+  const projectRoot = process.cwd()
+  fs.mkdirSync('some-directory', { recursive: true })
+  const subdirPath = path.join(projectRoot, 'some-directory')
+
+  await execPnpm(['install'])
+
+  const cmdFilePath = path.join(subdirPath, 'cwd.txt')
+
+  execPnpmSync(
+    ['exec', 'node', '-e', `require('fs').writeFileSync(${JSON.stringify(cmdFilePath)}, process.cwd(), 'utf8')`],
+    {
+      cwd: subdirPath,
+      expectSuccess: true,
+    }
+  )
+
+  expect(fs.readFileSync(cmdFilePath, 'utf8')).toBe(subdirPath)
+})