A novel approach for isomer depletion in ion-atom collisions is proposed and considered theoretically. Analyses are performed for the depletion of the ^{93m}Mo isomer for which an unexpectedly large probability was measured in the beam-based experiment of Chiara et al. [Nature (London) 554, 216 (2018)NATUAS0028-083610.1038/nature25483]. The subsequent attempt at a theoretical description based on state-of-the-art atomic theory did not reproduce the experimental result [Wu et al., Phys. Rev. Lett. 122, 212501 (2019)PRLTAO0031-900710.1103/PhysRevLett.122.212501] and showed a dramatic disagreement with the experiment (by many orders of magnitude). This conflict calls for further research on the nature of isomer depletion mechanisms occurring in atomic processes. Here, we propose to consider the ^{93m}Mo isomer depletion as the nuclear excitation by electron capture in resonant transfer process taking into account the momentum distribution of the target electrons. Although our results only slightly shift the upper theoretical limit for the total ^{93m}Mo isomer depletion probability toward the experimental value, they show the importance of considering the Compton profile in the theoretical description, in particular for the L shell, for which the depletion probability increases by many orders of magnitude.