diff --git a/.changeset/long-dryers-run.md b/.changeset/long-dryers-run.md
new file mode 100644
index 0000000000..55a71ee8c1
--- /dev/null
+++ b/.changeset/long-dryers-run.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/plugin-commands-publishing": patch
+---
+
+Scripts should be executed upon the original package.json, when publishConfig.directory is set.
diff --git a/packages/plugin-commands-publishing/src/pack.ts b/packages/plugin-commands-publishing/src/pack.ts
index 4c7337626c..73c9fe7ff6 100644
--- a/packages/plugin-commands-publishing/src/pack.ts
+++ b/packages/plugin-commands-publishing/src/pack.ts
@@ -64,7 +64,7 @@ export async function handler (
     workspaceDir?: string
   }
 ) {
-  const { manifest } = await readProjectManifest(opts.dir, opts)
+  const { manifest: entryManifest } = await readProjectManifest(opts.dir, opts)
   const _runScriptsIfPresent = runScriptsIfPresent.bind(null, {
     depPath: opts.dir,
     extraBinPaths: opts.extraBinPaths,
@@ -80,25 +80,29 @@ export async function handler (
       'prepare',
       'prepublishOnly',
       'prepack',
-    ], manifest)
+    ], entryManifest)
   }
+  const dir = entryManifest.publishConfig?.directory
+    ? path.join(opts.dir, entryManifest.publishConfig.directory)
+    : opts.dir
+  const manifest = (opts.dir !== dir) ? (await readProjectManifest(dir, opts)).manifest : entryManifest
   const tarballName = `${manifest.name!.replace('@', '').replace('/', '-')}-${manifest.version!}.tgz`
-  const files = await packlist({ path: opts.dir })
-  const filesMap: Record<string, string> = fromPairs(files.map((file) => [`package/${file}`, path.join(opts.dir, file)]))
-  if (opts.workspaceDir != null && opts.dir !== opts.workspaceDir && !files.some((file) => /LICEN[CS]E(\..+)?/i.test(file))) {
+  const files = await packlist({ path: dir })
+  const filesMap: Record<string, string> = fromPairs(files.map((file) => [`package/${file}`, path.join(dir, file)]))
+  if (opts.workspaceDir != null && dir !== opts.workspaceDir && !files.some((file) => /LICEN[CS]E(\..+)?/i.test(file))) {
     const licenses = await findLicenses({ cwd: opts.workspaceDir })
     for (const license of licenses) {
       filesMap[`package/${license}`] = path.join(opts.workspaceDir, license)
     }
   }
   const destDir = opts.packDestination
-    ? (path.isAbsolute(opts.packDestination) ? opts.packDestination : path.join(opts.dir, opts.packDestination ?? '.'))
-    : opts.dir
-  await packPkg(path.join(destDir, tarballName), filesMap, opts.dir)
+    ? (path.isAbsolute(opts.packDestination) ? opts.packDestination : path.join(dir, opts.packDestination ?? '.'))
+    : dir
+  await packPkg(path.join(destDir, tarballName), filesMap, dir)
   if (!opts.ignoreScripts) {
-    await _runScriptsIfPresent(['postpack'], manifest)
+    await _runScriptsIfPresent(['postpack'], entryManifest)
   }
-  return tarballName
+  return path.relative(opts.dir, path.join(dir, tarballName))
 }
 
 async function packPkg (destFile: string, filesMap: Record<string, string>, projectDir: string): Promise<void> {
diff --git a/packages/plugin-commands-publishing/src/publish.ts b/packages/plugin-commands-publishing/src/publish.ts
index 0ca1027554..1525462c1d 100644
--- a/packages/plugin-commands-publishing/src/publish.ts
+++ b/packages/plugin-commands-publishing/src/publish.ts
@@ -172,21 +172,20 @@ Do you want to continue?`,
     }
   }
 
-  const cwd = manifest.publishConfig?.directory ? path.join(dir, manifest.publishConfig.directory) : dir
-  const localNpmrc = path.join(cwd, '.npmrc')
+  const tarballName = await pack.handler({
+    ...opts,
+    dir,
+  })
+  const tarballDir = path.dirname(path.join(dir, tarballName))
+  const localNpmrc = path.join(tarballDir, '.npmrc')
   const copyNpmrc = !existsSync(localNpmrc) && opts.workspaceDir && existsSync(path.join(opts.workspaceDir, '.npmrc'))
   if (copyNpmrc && opts.workspaceDir) {
     await fs.copyFile(path.join(opts.workspaceDir, '.npmrc'), localNpmrc)
   }
-
-  const tarballName = await pack.handler({
-    ...opts,
-    dir: cwd,
+  const { status } = runNpm(opts.npmPath, ['publish', '--ignore-scripts', path.basename(tarballName), ...args], {
+    cwd: tarballDir,
   })
-  const { status } = runNpm(opts.npmPath, ['publish', '--ignore-scripts', tarballName, ...args], {
-    cwd,
-  })
-  await rimraf(path.join(cwd, tarballName))
+  await rimraf(path.join(dir, tarballName))
   if (copyNpmrc) {
     await rimraf(localNpmrc)
   }
diff --git a/packages/plugin-commands-publishing/test/publish.ts b/packages/plugin-commands-publishing/test/publish.ts
index 8d8c2f002d..0355773bb4 100644
--- a/packages/plugin-commands-publishing/test/publish.ts
+++ b/packages/plugin-commands-publishing/test/publish.ts
@@ -1,4 +1,4 @@
-import { promises as fs } from 'fs'
+import { existsSync, promises as fs } from 'fs'
 import path from 'path'
 import execa from 'execa'
 import isCI from 'is-ci'
@@ -297,6 +297,10 @@ test('publish: package with publishConfig.directory', async () => {
       name: 'test-publish-config-directory',
       version: '1.0.0',
 
+      scripts: {
+        prepublishOnly: 'node --eval="const fs=require(\'fs\');fs.mkdirSync(\'dist\',{recursive:true});fs.writeFileSync(\'dist/prepublishOnly\', \'\', \'utf8\')"',
+      },
+
       publishConfig: {
         directory: 'dist',
       },
@@ -311,12 +315,10 @@ test('publish: package with publishConfig.directory', async () => {
 
   await fs.writeFile(
     path.join(testPublishConfigDirectory.dir(), 'dist/package.json'),
-    `
-    {
-      "name": "publish_config_directory_dist_package",
-      "version": "1.0.0"
-    }
-  `,
+    JSON.stringify({
+      name: 'publish_config_directory_dist_package',
+      version: '1.0.0',
+    }),
     {
       encoding: 'utf-8',
     }
@@ -340,6 +342,7 @@ test('publish: package with publishConfig.directory', async () => {
       name: 'publish_config_directory_dist_package',
       version: '1.0.0',
     })
+  expect(existsSync('node_modules/publish_config_directory_dist_package/prepublishOnly')).toBeTruthy()
 })
 
 test.skip('publish package that calls executable from the workspace .bin folder in prepublishOnly script', async () => {