The ability to fully exploit redundant control capabilities available in aircraft is a critical feature in dealing with actuator failure scenarios. Managing input redundancy is traditionally addressed by means of Control Allocation (CA), where the aerodynamic control surfaces are typically considered only as moment-producing devices, thereby neglecting body forces, thus limiting a priori the possibilities offered by control reconfiguration. In the work presented in this thesis, we present a novel fault-tolerant control architecture for fixed-wing over-actuated and classical configuration small UAVs, where coupling between aerodynamic effectors and body forces are considered. The control architecture includes an adaptive loop for stable tracking of airspeed, flight path, and turn rate reference trajectories in nominal conditions (no actuator failures) in the presence of model parameter uncertainty. Fault tolerance is provided by a Dynamic Control Allocation (DCA) mechanism that automatically redistributes the control commands to the effectors as well as modifies certain reference trajectories to maintain the stability of the aircraft under multiple actuator failures. The particular design of the allocator makes fault identification algorithms unnecessary, simplifying the overall structure of the CA technique. In support of the theoretical development of this novel methodology, two case studies are presented. In the first case study, we consider flight simulations of a conceptual small over actuated UAV, which incorporates all the characteristics and the control architecture needed for the full exploitation of the flight control system herein developed. In the second test case, we consider real flight tests performed on a classical general aviation RC aircraft, which uses flaps as redundant control surfaces for roll control. Results are presented for different flights where ailerons are externally driven to move by 50% of the commanded deflection or not to move at all, simulating real ailerons failure conditions. Characterization of the environmental conditions is provided for each flight test in terms of normal accelerations, to quantify the level of perturbations faced by the flight controller. Simulation results are provided to demonstrate the performance and reliability of the control architecture, while flight test results are analyzed to confirm the robustness of the scheme against parameter uncertainty, actuation failure, and disturbance rejection.