Variations in the intensity of the incident beam can cause significant inaccuracies in microscopes that use focused beams of electrons or ions. Existing mitigation methods depend on the artifacts having characteristic spatial structures explained by the raster scan pattern and temporal correlation of the beam current variations. We show that recently introduced time-resolved measurement methods create robustness to beam current variations that improve significantly upon existing methods while not depending on separability of artifact structure from underlying image content. These advantages are illustrated through Monte Carlo simulations representative of both helium ion microscopy (higher secondary electron yield) and scanning electron microscopy (lower secondary electron yield). Notably, this demonstrates that when the beam current variation is appreciable, time-resolved measurements provide a novel benefit in particle beam microscopy that extends to low secondary electron yields.