The colonies of honey bees are mostly sessile organisms. Consequently, the type of nest boxes that beekeepers provide to their bees should impact a colony’s ability to maintain homeostasis, which is a key determinant of performance and fitness. Here, we used European honey bees (Apis mellifera) and provided them with two hive setups widely used and known as Langstroth and Warré. We compared colony performance in a Mediterranean climate for five months from late spring to early autumn, which covered the most active time of bees and included periods of heat and drought. We found that irrespective of hive type or season, honey bees kept hive temperature and humidity within a remarkably narrow range. Nevertheless, the hive type impacted the daily fluctuations in temperature and humidity. In Warré hives, where bees have more autonomy to build and maintain their combs, we found that bees were able to reduce daily fluctuations in temperature and humidity and kept both measures closer to the overall average. This increase in colony homeostasis found in Warré hives negatively correlated with other hive performance indicators, such as immunocompetence. We conclude that different hive types affect key areas, such as the central part of the colony with frames of developing brood or the queen, which are the most susceptible individuals. This implies that climatic changes resulting in extreme weather events are expected to impact colony performance and fitness, especially in non-managed honey bees that are limited by available nesting sites. For managed bees, adaptations to existing hive setups could be provided to help bees minimize the effects of abiotic stress.