Of all the current detection techniques with nanometre resolution, only X-ray microscopy allows imaging of nanoparticles in suspension. Can it also be used to investigate structural dynamics? When studying the response to mechanical stimuli, the challenge lies in its application with a precision comparable with the spatial resolution. In the first shear experiments performed in an X-ray microscope, this has been accomplished by inserting a piezo actuator driven shear cell into the focal plane of a scanning transmission X-ray microscope. Thus shear-induced re-organization of magnetite nanoparticle aggregates could be demonstrated in suspension. As X-ray microscopy proves suitable for studying structural change, new prospects open up in physics at small length scales.