Quantum control experiments are often subject to coherent, time-dependent disturbances that vary over timescales comparable to the experiment duration. We show that when such disturbances are reproducible with respect to a trigger signal, their effect can be measured and compensated through software-defined updates to the control frequency and phase. We experimentally verify the performance of our protocol using a trapped 137Ba+ ion experiencing magnetic-field-induced energy shifts synchronous with the laboratory AC mains power. Using this compensation technique, the calibrated AC line contribution to the instantaneous oscillator detuning is reduced by 21(9)x, and the fitted AC-induced phase amplitude is reduced below the measurement uncertainty. We also extend the compensation framework to multi-level qudit control. Using the Bernstein-Vazirani algorithm as a benchmark, we increase the algorithm’’s success probability from 10(7)% to 70(9)% in a 16-level system when compensation is enabled. Our results demonstrate that trigger-synchronized coherent errors can be re-framed as deterministic control-frame errors and corrected in software.