Free-electron lasers (FELs) provide unique possibilities in investigating matter down to femtosecond time and nanometer length scales, as well as in the regime of non-linear light-matter interaction. Due to the nature of FEL sources, the produced beam is significantly more unstable than beams produced by 3rd generation synchrotrons. As a result, pulse-resolved normalization of measurement data becomes essential and can be challenging. The intensity monitors permanently installed at a facility might indeed accurately measure the pulse intensities at a certain point of the beamline, but cannot precisely normalize experimental data. For example the impact of pointing instabilities and hence different clipping of the beam downstream on the way to the actual experiment is not reflected in the intensity measurement. Here, we show how the integral intensity of the FEL beam transmitted through the sample can be measured by photodiodes providing a proper normalization of measurement data.