This work shows how to use a differential geometry tool to design a novel nonlinear active fault tolerant flight control system for aircraft. The proposed control scheme consists of two main subsystems: a controller, which is designed for the nominal plant, and a fault detection and diagnosis module, which provides fault estimation. A further feedback loop exploits the fault estimation to accommodate faults affecting the system. The estimate convergence and the stability of the active fault tolerant flight controller are theoretically proved. Finally, high fidelity simulations show the effectiveness of the scheme. •Extension of nonlinear geometric approach to active fault tolerant control system.•Proofs of convergence of fault estimation for active fault tolerant control system.•New results in estimation of actuators fault decoupled from wind gusts.•New nominal controller design procedure with assured stability properties.•Proof of stability of active fault tolerant control system.