Non-migratory bats in colder climates use hibernation to survive winter. By reducing metabolic rate (i.e., using torpor), bats can survive winter on stored fat reserves. During hibernation, bats arouse from torpor and may move within the hibernaculum, a process called “internal migration”. We hypothesized that internal migration occurs to optimize hibernation energetics in that bats move to select a microclimate to minimize energy expenditure both by seeking cooler areas of the hibernacula and avoiding those with large temperature fluctuations. Early in the winter, we observed that 62% of bats were roosting in the warmer, less energy efficient, deepest 50% of an abandoned mine hibernaculum. Late in the season, there was a shift towards the cooler entrance area, thereby decreasing energy demands during the torpid period, with 78% of bats in the mine roosting within 50 m of the entrance. Although there was no significant effect of hibernation period (i.e., early vs. late winter) on the number of bats in huddles, the largest huddles occurred close to the entrance in late winter. To fully understand and manage bat populations, it is important to understand that hibernation is a dynamic process with bats moving and interacting with one another throughout the season.