The influence of the crystal structure and chemical nature of some ionic liquid/phosphomolybdate hybrids on their catalytic activity in the epimerization of glucose was studied. A clear evidence of structure–activity relationship was found. The inorganic part of the hybrid ensured the availability of active sites for the reaction, while the organic cation part organized the structure and controled the diffusion of the reactants. This study can be used as a first approach to predict the symmetry, long range order and availability of active sites in the presented class of imidazolium based polyoxometalate hybrids.