The main component of flow machines is the rotor; however, there may also be stationary parts surrounding the rotor, which are the diffuser blades. In order to consider these two parts simultaneously, the most intuitive approach is to perform a transient flow simulation; however, the computational cost is relatively high. Therefore, one possible approach is the Multiple Reference Frame (MRF) approach, which considers two directly coupled zones: one for the rotating reference frame (for the rotor blades) and one for the stationary reference frame (for the diffuser blades). When taking into account topology optimisation, some changes are required in order to take both rotating and stationary parts simultaneously in the design, which also leads to changes in the composition of the multi-objective function. Therefore, the topology optimisation method is formulated for MRF while also proposing this new multi-objective function. An integer variable-based optimisation algorithm is considered, with some adjustments for the MRF case. Some numerical examples are presented.