I have MVC controllers (in Controllers folder) and Web Api controllers (in Api folder) in the same project: Here is the folder structure:
You haven't set Web API's GlobalConfiguration.Configuration.DependencyResolver; you only set MVC's DependencyResolver.
GlobalConfiguration.Configuration.DependencyResolver
DependencyResolver
Add the following line:
GlobalConfiguration.Configuration.DependencyResolver = new AutofacWebApiDependencyResolver(container);