A major challenge in autonomous flights is unknown disturbances, which can jeopardize safety and lead to collisions, especially in obstacle-rich environments. This paper presents a disturbance-aware motion planning and control framework designed for autonomous aerial flights. The framework is composed of two key components: a disturbance-aware motion planner and a tracking controller. The disturbance-aware motion planner consists of a predictive control scheme and a learned model of disturbances that is adapted online. The tracking controller is designed using contraction control methods to provide safety bounds on the quadrotor behaviour in the vicinity of the obstacles with respect to the disturbance-aware motion plan. Finally, the algorithm is tested in simulation scenarios with a quadrotor facing strong crosswind and ground-induced disturbances.