Purpose: The paper aims to address the combined attitude control and Sun tracking problem in a flexible spacecraft in the presence of external and internal disturbances. The attitude stabilization of a flexible satellite is generally a challenging control problem, because of the facts that satellite kinematic and dynamic equations are inherently nonlinear, the rigid–flexible coupling dynamical effect, as well as the uncertainty that arises from the effect of actuator anomalies. Design/methodology/approach: To deal with these issues in the combined attitude and Sun tracking system, a novel control scheme is proposed based on the adaptive fuzzy Jacobian approach. The augmented spacecraft model is then analyzed and the Lyapunov-based backstepping method is applied to develop a nonlinear three-axis attitude pointing control law and the adaptation law. Findings: Numerical results show the effectiveness of the proposed adaptive control scheme in simultaneously tracking the desired attitude and the Sun. Practical implications: Reaction wheels are commonly used in many spacecraft systems for the three-axis attitude control by delivering precise torques. If a reaction wheel suffers from an irreversible mechanical breakdown, then it is likely going to interrupt the mission, or even leading to a catastrophic loss. The pitch-axis mounted solar array drive assemblies (SADAs) can be exploited to anticipate such situation to generate a differential torque. As the solar panels are rotated by the SADAs to be orientated relative to the Sun, the pitch-axis wheel control torque demand can be compensated by the differential torque. Originality/value: The proposed Jacobian control scheme is inspired by the knowledge of Jacobian matrix in the trajectory tracking of robotic manipulators. © 2020, Emerald Publishing Limited.