Traffic management for large-scale urban road networks remains a challenging problem. Aggregated dynamical models of city-scale traffic, based on the macroscopic fundamental diagram (MFD), enable development of model-based control schemes for use with the perimeter control method involving actuation over macroscopic traffic flows, specifying an efficient and practicable congestion control solution. In this paper we propose a nonlinear model predictive control scheme with guaranteed closed-loop stability for a two-region MFDs system. Extensive macroscopic simulations demonstrate the performance and region of attraction properties of the proposed method.