diff --git a/pnpm/test/updateInjectedPackagesAfterRun.ts b/pnpm/test/updateInjectedPackagesAfterRun.ts
new file mode 100644
index 0000000000..5877c789f1
--- /dev/null
+++ b/pnpm/test/updateInjectedPackagesAfterRun.ts
@@ -0,0 +1,289 @@
+import fs from 'fs'
+import path from 'path'
+import { preparePackages } from '@pnpm/prepare'
+import { type ProjectManifest } from '@pnpm/types'
+import { sync as writeYamlFile } from 'write-yaml-file'
+import { execPnpm } from './utils'
+
+const TEMPLATE_PACKAGE_NAMES = ['foo', 'bar', 'baz'] as const
+const TEMPLATE_FILE_NAMES = ['build1.cjs', 'build2.cjs', 'should-be-deleted-by-build1.txt', 'should-be-modified-by-build1.txt'] as const
+
+const template = {
+  manifests: (): Record<typeof TEMPLATE_PACKAGE_NAMES[number], ProjectManifest> => ({
+    foo: {
+      name: 'foo',
+      version: '0.0.0',
+      dependencies: {
+        'is-positive': '1.0.0',
+      },
+      scripts: {
+        build1: 'node ./build1.cjs',
+        build2: 'node ./build2.cjs',
+      },
+    },
+    bar: {
+      name: 'bar',
+      version: '0.0.0',
+      dependencies: {
+        foo: 'workspace:*',
+      },
+      scripts: {
+        build1: 'node ./build1.cjs',
+        build2: 'node ./build2.cjs',
+      },
+    },
+    baz: {
+      name: 'baz',
+      version: '0.0.0',
+      dependencies: {
+        bar: 'workspace:*',
+      },
+      scripts: {
+        build1: 'node ./build1.cjs',
+        build2: 'node ./build2.cjs',
+      },
+    },
+  }),
+  files: (): Record<typeof TEMPLATE_FILE_NAMES[number], string> => ({
+    'build1.cjs': `
+      const fs = require('fs')
+      fs.rmSync('should-be-deleted-by-build1.txt', { force: true })
+      fs.writeFileSync('should-be-modified-by-build1.txt', 'After modification')
+      fs.writeFileSync('should-be-added-by-build1.txt', __filename)
+    `,
+    'build2.cjs': `
+      const fs = require('fs')
+      fs.writeFileSync('created-by-build2.txt', __filename)
+    `,
+    'should-be-deleted-by-build1.txt': '',
+    'should-be-modified-by-build1.txt': 'Before modification',
+  }),
+  npmrc: (...suffix: string[]): string => [
+    'reporter=append-only',
+    'inject-workspace-packages=true',
+    'dedupe-injected-deps=false',
+    ...suffix,
+  ].join('\n'),
+}
+
+test('update-injected-files-after-run=true', async () => {
+  const manifests = template.manifests()
+  preparePackages(
+    TEMPLATE_PACKAGE_NAMES.map(pkgName => ({
+      location: `packages/${pkgName}`,
+      package: manifests[pkgName],
+    }))
+  )
+
+  const files = template.files()
+  for (const pkgName of TEMPLATE_PACKAGE_NAMES) {
+    for (const fileName of TEMPLATE_FILE_NAMES) {
+      fs.writeFileSync(path.join('packages', pkgName, fileName), files[fileName])
+    }
+  }
+
+  writeYamlFile('pnpm-workspace.yaml', {
+    packages: ['packages/*'],
+  })
+
+  const npmrc = template.npmrc('update-injected-files-after-run=true')
+  fs.writeFileSync('.npmrc', npmrc)
+
+  await execPnpm(['install'])
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('foo@file+packages+foo')
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('bar@file+packages+bar')
+  expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+  expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+
+  // build1 should update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build1'])
+
+    // injected foo
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).not.toContain('should-be-deleted-by-build1.txt')
+    expect(
+      fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-added-by-build1.txt', 'utf-8')
+    ).toBe(path.resolve('packages/foo/build1.cjs'))
+    expect(
+      fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-modified-by-build1.txt', 'utf-8')
+    ).toBe('After modification')
+
+    // injected bar
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).not.toContain('should-be-deleted-by-build1.txt')
+    expect(
+      fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-added-by-build1.txt', 'utf-8')
+    ).toBe(path.resolve('packages/bar/build1.cjs'))
+    expect(
+      fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-modified-by-build1.txt', 'utf-8')
+    ).toBe('After modification')
+  }
+
+  // build2 should update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build2'])
+
+    // injected foo
+    expect(
+      fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/created-by-build2.txt', 'utf-8')
+    ).toBe(path.resolve('packages/foo/build2.cjs'))
+
+    // injected bar
+    expect(
+      fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/created-by-build2.txt', 'utf-8')
+    ).toBe(path.resolve('packages/bar/build2.cjs'))
+  }
+})
+
+test('update-injected-files-after-run=false', async () => {
+  const manifests = template.manifests()
+  preparePackages(
+    TEMPLATE_PACKAGE_NAMES.map(pkgName => ({
+      location: `packages/${pkgName}`,
+      package: manifests[pkgName],
+    }))
+  )
+
+  const files = template.files()
+  for (const pkgName of TEMPLATE_PACKAGE_NAMES) {
+    for (const fileName of TEMPLATE_FILE_NAMES) {
+      fs.writeFileSync(path.join('packages', pkgName, fileName), files[fileName])
+    }
+  }
+
+  writeYamlFile('pnpm-workspace.yaml', {
+    packages: ['packages/*'],
+  })
+
+  const npmrc = template.npmrc('update-injected-files-after-run=false')
+  fs.writeFileSync('.npmrc', npmrc)
+
+  await execPnpm(['install'])
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('foo@file+packages+foo')
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('bar@file+packages+bar')
+  expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+  expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+
+  // build1 should not update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build1'])
+
+    // injected foo
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).toContain('should-be-deleted-by-build1.txt')
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).not.toContain('should-be-added-by-build1.txt')
+
+    // injected bar
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).toContain('should-be-deleted-by-build1.txt')
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).not.toContain('should-be-added-by-build1.txt')
+  }
+
+  // build2 should not update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build2'])
+
+    // injected foo
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).not.toContain('created-by-build2.txt')
+
+    // injected bar
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).not.toContain('created-by-build2.txt')
+  }
+})
+
+test('filter scripts', async () => {
+  const manifests = template.manifests()
+  preparePackages(
+    TEMPLATE_PACKAGE_NAMES.map(pkgName => ({
+      location: `packages/${pkgName}`,
+      package: manifests[pkgName],
+    }))
+  )
+
+  const files = template.files()
+  for (const pkgName of TEMPLATE_PACKAGE_NAMES) {
+    for (const fileName of TEMPLATE_FILE_NAMES) {
+      fs.writeFileSync(path.join('packages', pkgName, fileName), files[fileName])
+    }
+  }
+
+  writeYamlFile('pnpm-workspace.yaml', {
+    packages: ['packages/*'],
+  })
+
+  const npmrc = template.npmrc('update-injected-files-after-run[]=build1')
+  fs.writeFileSync('.npmrc', npmrc)
+
+  await execPnpm(['install'])
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('foo@file+packages+foo')
+  expect(fs.readdirSync('node_modules/.pnpm')).toContain('bar@file+packages+bar')
+  expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+  expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar').sort()).toStrictEqual([
+    ...TEMPLATE_FILE_NAMES,
+    'package.json',
+  ].sort())
+  expect(
+    fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-modified-by-build1.txt', 'utf-8')
+  ).toBe('Before modification')
+
+  // build1 should update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build1'])
+
+    // injected foo
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).not.toContain('should-be-deleted-by-build1.txt')
+    expect(
+      fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-added-by-build1.txt', 'utf-8')
+    ).toBe(path.resolve('packages/foo/build1.cjs'))
+    expect(
+      fs.readFileSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo/should-be-modified-by-build1.txt', 'utf-8')
+    ).toBe('After modification')
+
+    // injected bar
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).not.toContain('should-be-deleted-by-build1.txt')
+    expect(
+      fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-added-by-build1.txt', 'utf-8')
+    ).toBe(path.resolve('packages/bar/build1.cjs'))
+    expect(
+      fs.readFileSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar/should-be-modified-by-build1.txt', 'utf-8')
+    ).toBe('After modification')
+  }
+
+  // build2 should not update the injected files
+  {
+    await execPnpm(['--recursive', 'run', 'build2'])
+
+    // injected foo
+    expect(fs.readdirSync('node_modules/.pnpm/foo@file+packages+foo/node_modules/foo')).not.toContain('created-by-build2.txt')
+
+    // injected bar
+    expect(fs.readdirSync('node_modules/.pnpm/bar@file+packages+bar/node_modules/bar')).not.toContain('created-by-build2.txt')
+  }
+})