Aerial humanoid robots can enhance the efficiency and safety of rescue operations in disaster scenarios. The control of such complex machines presents many challenges, for instance, the control of the different locomotion strategies and the stabilization of the transition maneuvers. In this article, we present an online nonlinear Model Predictive Controller and the relative prediction model to stabilize walking and flying trajectories. The controller uses a reduced model to generate feasible base link references, thrust profiles, and contact forces while dealing with different locomotion strategies and transition maneuvers. The control algorithm is tested in a simulated environment using our aerial humanoid robot iRonCub under the effect of external disturbances. The proposed control strategy demonstrates to effectively stabilize the desired trajectories while keeping the problem still treatable online.