diff --git a/.changeset/tidy-teeth-accept.md b/.changeset/tidy-teeth-accept.md
new file mode 100644
index 0000000000..6156b1e508
--- /dev/null
+++ b/.changeset/tidy-teeth-accept.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/package-store": patch
+"pnpm": patch
+---
+
+`pnpm store prune` should not fail if the store contains Node.js packages [#10131](https://github.com/pnpm/pnpm/issues/10131).
diff --git a/store/package-store/src/storeController/prune.ts b/store/package-store/src/storeController/prune.ts
index 5dd36e1177..6caf5a90b3 100644
--- a/store/package-store/src/storeController/prune.ts
+++ b/store/package-store/src/storeController/prune.ts
@@ -75,7 +75,8 @@ export async function prune ({ cacheDir, storeDir }: PruneOptions, removeAlienFi
   let pkgCounter = 0
   await Promise.all(pkgIndexFiles.map(async (pkgIndexFilePath) => {
     const { files: pkgFilesIndex } = await readV8FileStrictAsync<PackageFilesIndex>(pkgIndexFilePath)
-    if (removedHashes.has(pkgFilesIndex['package.json'].integrity)) {
+    // TODO: implement prune of Node.js packages, they don't have a package.json file
+    if (pkgFilesIndex['package.json'] && removedHashes.has(pkgFilesIndex['package.json'].integrity)) {
       await fs.unlink(pkgIndexFilePath)
       pkgCounter++
     }