The effects of adding silica nanoparticles of varying size and surface chemistry to a liquid crystal system were analysed using small-angle scattering and polarising light microscopy, with varying temperature and applied shear. It was found that nanoparticles aggregate at domain boundaries, causing a reduction in average liquid crystal domain size. These particles can inhibit phase transitions that occur at specific temperatures, ascribed to aggregates posing a kinetic barrier to rearrangement required for phase transitions. Nanoparticles can also promote the existence of specific phases, such as a deswollen hexagonal mesophase for the system studied here, suggested to be caused by silica aggregates 'templating' new phases. These findings have important implications for the application of such systems in biotechnology, and particularly the ability to completely inhibit a phase change at low temperature suggests the potential for mechanistic insight into new methods of cryopreservation.