This paper addresses the development of a novel Active Fault Tolerant Control Scheme (AFTCS) which, when used with an independently designed guidance system, turns out to give an overall fault tolerant guidance and control system. This AFTCS methodology avoids a logic-based switching controller by exploiting an adaptive fault estimator whose design is based on the Non Linear Geometric Approach (NLGA). The application of the AFTC scheme to a Piper PA-30 aircraft simulator in a flight condition characterized by a tight-coupled longitudinal and lateral dynamics even in presence of wind, shows the enhancement of the flying quality, the asymptotic fault accommodation and the control objective recovery.