This paper introduces a new experimental method to monitor the evolving intra-particle, nanometre-scale response during hydro-mechanical tests on undisturbed wet clay samples using small angle X-ray scattering (SAXS). The method uses a newly developed miniature plane-strain one-dimensional compression cell that facilitates simultaneous full-field surface displacement measurements using digital image correlation and SAXS measurements. The 60–120 s acquisition times offered by SAXS at synchrotron facilities are beneficial to study time-dependent mechanisms in clays. The experimental results presented indicate that, for the natural sensitive clay tested in this work, no significant structural changes occur at the intra-particle scale during loading, even when large strains are measured at the macro-scale. In addition, changes that are observed at this scale occur after the end of perturbation, i.e. the creation of new intra-particle structures. Further information is obtained on the orientation evolution of the fabric by the comparative analysis of the individual mineral component response.