diff --git a/pnpm/.changeset/clean-ci-workspace-state.md b/pnpm/.changeset/clean-ci-workspace-state.md
new file mode 100644
index 0000000000..6e23ce8462
--- /dev/null
+++ b/pnpm/.changeset/clean-ci-workspace-state.md
@@ -0,0 +1,5 @@
+---
+"pnpm": patch
+---
+
+Remove pnpm's workspace state file when cleaning node_modules so `pnpm ci` performs a fresh install after the clean step.
diff --git a/pnpm/src/cmd/clean.ts b/pnpm/src/cmd/clean.ts
index b0e4361039..2ca355f41d 100644
--- a/pnpm/src/cmd/clean.ts
+++ b/pnpm/src/cmd/clean.ts
@@ -103,7 +103,7 @@ async function cleanProjectDir (opts: { modulesDir: string, removeLockfile?: boo
   }
 }
 
-const PNPM_HIDDEN_ENTRIES = new Set(['.bin', '.modules.yaml', '.pnpm'])
+const PNPM_HIDDEN_ENTRIES = new Set(['.bin', '.modules.yaml', '.pnpm', '.pnpm-workspace-state-v1.json'])
 
 async function hasContentsToRemove (modulesDir: string): Promise<boolean> {
   let items: string[]
diff --git a/pnpm/test/clean.ts b/pnpm/test/clean.ts
index cc65d8eb89..572097b7d1 100644
--- a/pnpm/test/clean.ts
+++ b/pnpm/test/clean.ts
@@ -20,6 +20,7 @@ test('pnpm clean removes pnpm entries and packages but preserves non-pnpm hidden
   fs.mkdirSync('node_modules/.pnpm', { recursive: true })
   fs.mkdirSync('node_modules/.bin')
   fs.writeFileSync('node_modules/.modules.yaml', 'storeDir: /tmp/store')
+  fs.writeFileSync('node_modules/.pnpm-workspace-state-v1.json', '{}')
   fs.mkdirSync('node_modules/.cache')
   fs.writeFileSync('node_modules/.cache/some-file', 'cached')
   fs.mkdirSync('node_modules/lodash')
@@ -34,6 +35,7 @@ test('pnpm clean removes pnpm entries and packages but preserves non-pnpm hidden
   expect(fs.existsSync('node_modules/.pnpm')).toBe(false)
   expect(fs.existsSync('node_modules/.bin')).toBe(false)
   expect(fs.existsSync('node_modules/.modules.yaml')).toBe(false)
+  expect(fs.existsSync('node_modules/.pnpm-workspace-state-v1.json')).toBe(false)
 
   // Regular packages should be removed
   expect(fs.existsSync('node_modules/lodash')).toBe(false)