The combination of nonlinear indirect and direct adaptive control with an active fault-tolerant framework is proposed in this paper for quadrotor position tracking control under uncertain and fault conditions. An inner loop direct model reference adaptive controller generates the required force while moving along the reference trajectory, while nonlinear indirect adaptive controller maintains the required attitude angles. Furthermore, for uncertain conditions, our proposed framework provides significantly stable characteristics. Otherwise, when a fault occurs at actuators or sensors, the quadrotor vehicle cannot guarantee global asymptotic stability. This study contributes to an active fault-tolerant control strategy for solving the complex position tracking problem using the adaptive two-stage Kalman filter (ATSKF). Based on the fault information, a fault compensation term is added to the control law to improve convergence and system robustness in the presence of uncertain and fault conditions. Finally, simulation results show satisfactory performance for quadrotor vehicle position tracking, even with actuator faults and uncertainties.