In this paper, the performance of L1 adaptive control laws is investigated in the presence of aircraft actuator failures and atmospheric turbulence. L1 adaptive control is combined with a linear type controller and a nonlinear dynamic inversion-based outer/inner loop controller. Specific evaluation metrics are defined in terms of trajectory tracking errors and control activity during autonomous flight. Several types of trajectories with different levels of complexity are considered in this research effort. The West Virginia University unmanned aerial vehicle simulation environment is used in this analysis. The results show that the adaptive augmentation improves the tracking performance of the vehicle at nominal conditions and under a variety of abnormal flight conditions.