CLion won't show output in Debug

Putting setbuf(stdout, 0); before any printf statement or any output happens fixed this problem.

If you don't care to use the built-in clion console, you can solve the issue by changing the default debugger used by clion.

Under Settings => Toolchain => <your compiler> => Debugger change Bundled GDB to your compiler's debugger, e.g. MinGW: