diff --git a/workspaces/config/lib/index.js b/workspaces/config/lib/index.js
index fda049fe08535..e46fe3d2aa2f3 100644
--- a/workspaces/config/lib/index.js
+++ b/workspaces/config/lib/index.js
@@ -610,7 +610,15 @@ class Config {
     process.emit('time', 'config:load:file:' + file)
     // only catch the error from readFile, not from the loadObject call
     await readFile(file, 'utf8').then(
-      data => this.#loadObject(ini.parse(data), type, file),
+      data => {
+        const parsedConfig = ini.parse(data)
+        if (type === 'project' && parsedConfig.prefix) {
+          // Log error if prefix is mentioned in project .npmrc
+          /* eslint-disable-next-line max-len */
+          log.error('config', `prefix cannot be changed from project config: ${file}.`)
+        }
+        return this.#loadObject(parsedConfig, type, file)
+      },
       er => this.#loadObject(null, type, file, er)
     )
     process.emit('timeEnd', 'config:load:file:' + file)
diff --git a/workspaces/config/test/index.js b/workspaces/config/test/index.js
index 520d554436ea8..9e9fac4f6dc34 100644
--- a/workspaces/config/test/index.js
+++ b/workspaces/config/test/index.js
@@ -1447,3 +1447,34 @@ t.test('umask', async t => {
     t.equal(umask, 0)
   })
 })
+
+t.test('catch project config prefix error', async t => {
+  const path = t.testdir()
+  t.testdir({
+    project: {
+      node_modules: {},
+      '.npmrc': `
+      project-config = true
+      foo = from-project-config
+      prefix=./lib
+      `,
+    },
+  })
+  const config = new Config({
+    npmPath: `${path}/npm`,
+    argv: [process.execPath, __filename, '--projectconfig', `${path}/project/.npmrc`],
+    cwd: join(`${path}/project`),
+    shorthands,
+    definitions,
+  })
+  const logs = []
+  const logHandler = (...args) => logs.push(args)
+  process.on('log', logHandler)
+  t.teardown(() => process.off('log', logHandler))
+  logs.length = 0
+  // config.load() triggers the error to be logged
+  await config.load()
+  t.match(logs, [[
+    'error', 'config', `prefix cannot be changed from project config: ${path}`,
+  ]], 'Expected error logged')
+})