Light millicharged particles can be copiously produced from meson decays in cosmic ray collisions with the atmosphere, leading to detectable signals in large underground neutrino detectors. In this paper we study a new channel for generating atmospheric millicharged particles, the proton bremsstrahlung process. We find that the proton bremsstrahlung process leads to a significantly higher flux of millicharged particles compared to meson decays and, for certain masses, results in a one-order-of-magnitude improvement in the flux. Consequently, Super-K constraints on ε2 for sub-GeV MCPs are improved by half order of magnitude. We further note that the study on the proton bremsstrahlung process can be extended to a variety of new physics particle searches in atmospheric collisions and in low energy proton accelerators.