A fraction of light scalar dark matter, especially axions, may organize into Bose-Einstein condensates, gravitationally bound clumps, boson stars, and be present in large number in galactic halos today. We compute the expected number of gravitational microlensing events of clumps composed of the ordinary QCD axion and axion-like-particles and derive microlensing constraints from the EROS-2 survey and the Subaru Hyper Suprime-Cam observation. We perform a detailed lensing calculation, including the finite lens and source size effects in our analysis. We constrain the axion mass in terms of the fraction of dark matter collapsed into clumps, the individual clump densities, and the axion self-coupling. We also consider and constrain clumps composed of a generic scalar dark matter candidate with repulsive self-interactions. Our analysis opens up a new window for the potential discovery of dark matter.