Variations in weather impact the energy budgets of endotherms depending on specific ecophysiology. While much focus has been on the thermal physiology of species that experience cold temperate winters, less is known about responses by species that experience subtle changes in seasonal weather patterns. We monitored summer skin temperatures (Tsk) of individuals from a North (Pureora) and South Island (Eglinton) population of New Zealand lesser short-tailed bats (Mystacina tuberculata), and winter Tsk patterns of individuals from Pureora and an offshore island (Hauturu) population using temperature telemetry. Summer Ta was only <2°C lower for the Eglinton population relative to Pureora yet Eglinton individuals used torpor on 36% of days compared to 11% for Pureora bats. Roosts housing solitary bats were warmer than those shared, and temperatures within them fluctuated less than Ta. Solitary roosts were occupied more often by Eglinton individuals (38%) than Pureora individuals (17%), with individuals from both populations occupying solitary roosts exclusively for torpor. During winter, despite a >6°C difference in mean Ta, neither torpor bout duration, nor minimum Tsk differed for individuals between sites. However, bats on Hauturu used short torpor (<24 hours) more frequently (51%) than in Pureora (33%). Hauturu bats preferred thermally unstable roosts and preferentially roosted inside dead punga (Cyathea dealbata). Site-specific roost choice and torpor patterns are apparent between M. tuberculata populations demonstrating Ta may differentially impact populations across a latitudinal gradient. Our results provide evidence that site and climate specific adaptations appear to be employed that affect roost choice and torpor patterns.