Multiphase machines have recently gained interest in the research community for their use in applications where high power density, wide speed range and fault-tolerant capabilities are required. The optimal control of such drives requires the consideration of voltage and current limits imposed by the power converter and the machine. While conventional three-phase drives have been extensively analyzed taking into account such limits, the same cannot be said in the multiphase drives’ case. This paper deals with this issue, where a novel two-stage Model Predictive optimal Control (2S-MPC) technique is presented, and a five-phase permanent magnet synchronous multiphase machine (PMSM) is used as a case example. The proposed method first applies a Continuous-Control-Set Model Predictive Control (CCS-MPC) stage to obtain the optimal real-time stator current reference for given DC-link voltage and stator current limits, exploiting the maximum performance characteristics of the multiphase drive. Then, a Finite-Control-Set Model Predictive Control (FCS-MPC) stage is utilized to generate the switching state in the power converter and force the stator current tracking. An experimental validation of the proposed controller is finally provided using a real-time simulation environment based on OPAL-RT technologies.