A computer-implemented method and system for controlling an aircraft based on detecting and mitigating fatiguing conditions and aircraft damage conditions is disclosed. According to one example, a computer-implemented method includes detecting, by a processing system, a health condition of a component of the aircraft. The method further includes determining, by the processing system, whether the health condition is one of a fatigue condition or a damage condition. The method further includes implementing, by the processing system, a first action based at least in part on determining that the health condition is a fatigue condition to mitigate the fatigue condition. The method further includes implementing, by the processing system, a second action based at least in part on determining that the health condition is a damage condition to mitigate the damage condition.