diff --git a/.changeset/violet-insects-attack.md b/.changeset/violet-insects-attack.md
new file mode 100644
index 0000000000..ed464c4e1a
--- /dev/null
+++ b/.changeset/violet-insects-attack.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/resolve-dependencies": patch
+"pnpm": patch
+---
+
+Fix the incorrect error block when subproject has been patched [#6183](https://github.com/pnpm/pnpm/issues/6183)
diff --git a/pkg-manager/resolve-dependencies/src/index.ts b/pkg-manager/resolve-dependencies/src/index.ts
index 9b98263e55..4f8386d84c 100644
--- a/pkg-manager/resolve-dependencies/src/index.ts
+++ b/pkg-manager/resolve-dependencies/src/index.ts
@@ -120,7 +120,7 @@ export async function resolveDependencies (
   // We only check whether patches were applied in cases when the whole lockfile was reanalyzed.
   if (
     opts.patchedDependencies &&
-    (opts.forceFullResolution || !opts.wantedLockfile.packages?.length) &&
+    (opts.forceFullResolution || !Object.keys(opts.wantedLockfile.packages ?? {})?.length) &&
     Object.keys(opts.wantedLockfile.importers).length === importers.length
   ) {
     verifyPatches({