This species is usually found in evergreen or pine-oak forest and pine forest at mid and high elevations, also at lower elevations in riparian habitats near desert scrub (Reid 2009). It roosts in tight clusters in caves, mine tunnels, buildings, and under bridges. These colonies can number from 50 to 15,000 individuals (Fitch et al. 1981, Reid 2009). This bat leaves the roost about 30 minutes after sunset and flies directly to water to drink before foraging. It usually forages just above the vegetation, with fast, direct flight. Females return to the day roost within 2 to 3 hours and feed again before dawn. Like most North American bats, this species is insectivorous, insects eaten include beetles, flying ants, and moths. Its diet changes with the season and habitat. The cave myotis normally feeds twice a night during the summer, once soon after sunset and again just before sunrise. Some northern populations hibernate in winter, others migrate. Populations in Mexico move to higher elevations in winter to hibernate (Wilson and Ruff 1999). In New Mexico, this species is active at temperatures (18 to 26 °C) higher than other species of Myotis, except M. yumanensis (17 to 27 °C). In Kansas, single young are born in June to July. In Veracruz, Mexico, pregnant females were caught in March and December (Hall and Dalquest 1963, Fitch et al. 1981, Reid 2009).Banding of M. velifer revealed their longevity to be at least 6 years, but it has been suggested that a 10 to 12 year life span would not be unreasonable (Fitch et al. 1981).

This species occurs from Honduras and Guatemala northward to Kansas, southern Nevada and southeastern California (USA) (Wilson and Ruff 1999, Simmons 2005). It occurs from lowlands to 3,300 m (Reid 2009).

Through its geographic distribution, this species occurs in several protected areas.