Yes, this setup is not recommended nor supported as .NET will identify the logically nested app and there could be some web.config conflicts or settings inheritance going on. While the front end app is MVC the admin is webforms and this can cause issues. It is recommended to run the apps side-by-side. Either separate domains = separate IIS sites or, if you need to keep single domain, use virtual apps on the same level: domain.com/frontendapp and domain.com/adminapp