The paper investigates the development of an active fault tolerant control strategy obtained from the integration of a fault detection and diagnosis module with a controller reconfiguration method. The methodology is based on a fault detection and diagnosis procedure relying on adaptive filters designed via a nonlinear approach. The controller reconfiguration mechanism exploited in the control loop relies on the on–line estimate of the fault signal. The active fault tolerant control scheme is applied to a simulator of an aerial vehicle in several flight conditions, in the presence of actuator faults, turbulence, measurement noise, and modelling errors.