This research presents an implementation of a novel controller design on an overactuated hybrid Unmanned Aerial Vehicle (UAV). This platform is a hybrid between a conventional quadcopter and a fixed-wing aircraft. Its inner loop is controlled by an existing but modified control method called Incremental Non-linear Control Allocation or INCA. This controller deals with the platform’s control allocation problem by minimising a set of objective functions with a method known as the Active Set Method and avoids actuator saturation. For the vehicle’s outer loop, a novel extension to INCA is presented, called Extended INCA or XINCA. This method optimises one of the physical actuator’s command and the angular control demands fed to the vehicle’s inner loop, based on linear reference accelerations. It does so while adapting to varying flight phases, conditions and vehicle states, and taking into account the aerodynamic properties of the main wing. XINCA has low dependence on accurate vehicle models and requires configuration using only several optimisation parameters. Both flight simulations and experimental flights are performed to prove the performance of both controllers.