diff --git a/.changeset/proud-lies-shout.md b/.changeset/proud-lies-shout.md
new file mode 100644
index 0000000000..0c7fca9f03
--- /dev/null
+++ b/.changeset/proud-lies-shout.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/config": patch
+---
+
+fix: remove empty keys from config key check
diff --git a/packages/config/src/index.ts b/packages/config/src/index.ts
index 3b784b75f2..50a8bf79e2 100644
--- a/packages/config/src/index.ts
+++ b/packages/config/src/index.ts
@@ -395,7 +395,7 @@ export default async (
   const settingKeys = Object.keys({
     ...npmConfig?.sources?.workspace?.data,
     ...npmConfig?.sources?.project?.data,
-  })
+  }).filter(key => key.trim() !== '')
   const unknownKeys = []
   for (const key of settingKeys) {
     if (!rcOptions.includes(key) && !key.startsWith('//') && !(key.startsWith('@') && key.endsWith(':registry'))) {
diff --git a/packages/config/test/index.ts b/packages/config/test/index.ts
index 391da5f33c..68d2bf4300 100644
--- a/packages/config/test/index.ts
+++ b/packages/config/test/index.ts
@@ -634,6 +634,7 @@ test('warn user unknown settings in npmrc', async () => {
   process.chdir(tmp)
   const npmrc = [
     'typo-setting=true',
+    ' ',
     'mistake-setting=false',
     '//foo.bar:_authToken=aaa',
     '@qar:registry=https://registry.example.org/',