The high, constant body temperatures of endotherms like birds and mammals are thought to facilitate the specialization of biochemical processes to warm temperatures. However, endotherms experience temperature variation (regional heterothermy) across body regions, even as they tightly regulate core temperature. As nocturnal fliers, small bats incur substantial heat loss from their poorly insulated wings via convection and radiative heat transfer to the night sky. Since rate-related processes in muscle slow at cooler temperatures, temperature effects in the wing muscles may impair flight performance and impact flight energetics. Although the cooling of these muscles during flight has implications for locomotor performance, peripheral cooling is rarely quantified in animals because of the logistical challenge posed by measuring body temperatures at multiple points on the trunk and limbs during active locomotion. In the field, surface temperatures measured through methods such as thermal imaging may not reflect the temperatures of deeper functional tissues, while measurements of core body temperature by subcutaneous or intraperitoneal loggers do not capture temperature variation across the body. Lab-based experiments, in which multiple regions of the body can be instrumented for in-flight measurements, may reduce or control for the environmental thermal heterogeneity that likely plays an important role in determining body temperatures in free-flying bats. Here, we demonstrate that bat wings are substantially cooler than the core, and discuss the challenges and benefits of our combined laboratory and field-based approach to expand our understanding of thermoregulatory strategy in bats during active locomotion.