Seems that if your project uses scripts while building to copy sources / headers, Xcode won't look into them to index because they don't exist under "Index" directory. The "Index Build" process will build project with Configuration: Null ( you can see in index build log ). So I think the solution here is that we have to re-write some rules in Build Phase and check if it is under indexing process, then modify target path. Of course, it is really disaster for me. Please, Xcode developer, fix this