Insects are some of the most adaptable fliers in nature as they readily adapt to changes in the environment and physical damage. The robustness of flying insects to wing damage is of particular interest since insects cannot repair wings. Thus, flying insects must rely on neuromechanical control strategies to compensate for wing damage. While insects can retain the ability to fly after wing damage, its effect on flight performance remains poorly understood. We conducted a frequency domain analysis of magnetically tethered fruit flies with intact and asymmetrically damaged wings (missing 10–40% of the wing area). In response to oscillating stimuli, the optomotor response of intact-wing flies was tuned to frequencies between 0.4–3 Hz. The optomotor response of both groups was strongest for frequencies between 0.2 and 1.5 Hz and was mostly attenuated at frequencies above 2.4 Hz. The phase lag decreased gradually with increasing frequency, suggesting a constant delay. A statistical comparison of the performance of both groups yielded a frequency-dependent influence of wing damage on flight response gain but not on phase. In addition, damaged-wing flies drifted in the direction of the damaged wing. During gaze stabilization, flies compensated for wing damage by decreasing the amplitude of the intact wing, whereas the amplitude of the damaged wing remained unchanged compared to the intact-wing group. Frequency domain analysis revealed that by using neuromechanical control strategies, fruit flies compensated partially for asymmetric damage but achieved diminished flight performance. A system identification framework can reveal performance tradeoffs and provide insights into how animals compensate for perturbations in an uncertain world.