diff --git a/.changeset/dull-poems-smoke.md b/.changeset/dull-poems-smoke.md
new file mode 100644
index 0000000000..ac5ef00421
--- /dev/null
+++ b/.changeset/dull-poems-smoke.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/plugin-commands-installation": minor
+---
+
+`pnpm prune` should remove the modules cache.
diff --git a/packages/plugin-commands-installation/src/prune.ts b/packages/plugin-commands-installation/src/prune.ts
index bb9b4726b6..8883271d8b 100644
--- a/packages/plugin-commands-installation/src/prune.ts
+++ b/packages/plugin-commands-installation/src/prune.ts
@@ -62,6 +62,7 @@ export async function handler (
       devDependencies: opts.dev !== false,
       optionalDependencies: opts.optional !== false,
     },
+    modulesCacheMaxAge: 0,
     pruneStore: true,
     storeController: store.ctrl,
     storeDir: store.dir,
diff --git a/packages/plugin-commands-installation/test/prune.ts b/packages/plugin-commands-installation/test/prune.ts
index 973616d98d..7f18612a46 100644
--- a/packages/plugin-commands-installation/test/prune.ts
+++ b/packages/plugin-commands-installation/test/prune.ts
@@ -73,5 +73,7 @@ test('prune removes dev dependencies', async () => {
   })
 
   await project.has('is-positive')
+  await project.has('.pnpm/is-positive@1.0.0')
   await project.hasNot('is-negative')
+  await project.hasNot('.pnpm/is-negative@1.0.0')
 })