If you have generated MEX code, generated code will by default have calls to FFTW library. However, if you are generating standalone code, code generator will produce code for FFT algorithms. If you have a FFTW library installed, please follow the instructions in the page Abstract class for specifying an FFTW library for FFTW calls in generated code - MATLAB (mathworks.com) to integrate the Library with MATLAB Coder generated code.