The .pro file is in the same directory as the Makefile, and since qmake generated the Makefile from the .pro file, it should get the path right on its own. Essentially, it's prepending a huge roundabout directory path in front of files inside the project, completely unneccessarily. If I manually remove the lengthy ../../../Users/talvala/Repositories/tmp/qthello/ section from all paths in the Makefile, it works fine. But that gets tedious very quickly, and qmake shouldn't be doing such a thing in any case - why doesn't it just encode the local relative paths, instead of what looks like an attempt to round-trip through 5 layers of directories?