A compact high-speed X-ray atomic force microscope has been developed for in situ use in normal-incidence X-ray experiments on synchrotron beamlines, allowing for simultaneous characterization of samples in direct space with nanometric lateral resolution while employing nanofocused X-ray beams. In the present work the instrument is used to observe radiation damage effects produced by an intense X-ray nanobeam on a semiconducting organic thin film. The formation of micrometric holes induced by the beam occurring on a timescale of seconds is characterized.