Social insects, such as ants, termites, and honeybees, have evolved sophisticated societies where collaboration and division of labor enhance survival of the whole colony, and are thus considered “superorganisms”. Historically, studying behaviors involving large groups under natural conditions posed significant challenges, often leading to experiments with a limited number of organisms under artificial laboratory conditions that incompletely reflected the animals’ natural habitat. A promising approach to exploring animal behaviors, beyond observation, is using robotics that produce stimuli to interact with the animals. However, their application has predominantly been constrained to small groups in laboratory conditions. Here we present the design choices and development of a biocompatible robotic system intended to integrate with complete honeybee colonies in the field, enabling exploration of their collective thermoregulatory behaviors via arrays of thermal sensors and actuators. We tested the system’s ability to capture the spatiotemporal signatures of two key collective behaviors. A 121-day observation revealed thermoregulation activity of the broodnest area during the foraging season, followed by clustering behavior during winter. Then we demonstrated the system’s ability to influence the colony by guiding a cluster of bees along an unnatural trajectory, via localized thermal stimuli emitted by two robotic frames. These results showcase a system with the capability to experimentally modulate honeybee colonies from within, as well as to unobtrusively observe their dynamics over extended periods. Such biohybrid systems uniting complete societies of thousands of animals and interactive robots can be used to confirm or challenge the existing understanding of complex animal collectives.