Unmanned aerial vehicles (UAVs) have the potential to revolutionize the way research is conducted in many scientific fields 1, 2. UAVs can access remote or difficult terrain 3, collect large amounts of data for lower cost than traditional aerial methods, and facilitate observations of species that are wary of human presence 4. Currently, despite large regulatory hurdles 5, UAVs are being deployed by researchers and conservationists to monitor threats to biodiversity 6, collect frequent aerial imagery 7–9, estimate population abundance 4, 10, and deter poaching 11. Studies have examined the behavioral responses of wildlife to aircraft 12–20 (including UAVs 21), but with the widespread increase in UAV flights, it is critical to understand whether UAVs act as stressors to wildlife and to quantify that impact. Biologger technology allows for the remote monitoring of stress responses in free-roaming individuals 22, and when linked to locational information, it can be used to determine events 19, 23, 24 or components of an animal’s environment 25 that elicit a physiological response not apparent based on behavior alone. We assessed effects of UAV flights on movements and heart rate responses of free-roaming American black bears. We observed consistently strong physiological responses but infrequent behavioral changes. All bears, including an individual denned for hibernation, responded to UAV flights with elevated heart rates, rising as much as 123 beats per minute above the pre-flight baseline. It is important to consider the additional stress on wildlife from UAV flights when developing regulations and best scientific practices. Display omitted •Cardiac biologgers reveal that bears exhibit a stress response to UAV flights•Bears rarely display a behavioral response, measured by GPS collars, to UAV flights•Magnitudes of heart rate spikes were correlated with wind speed and proximity of UAV Unmanned aerial vehicles (UAVs; i.e., “drones”) are increasingly popular tools for ecological research. Ditmer et al. used GPS collars and cardiac biologgers to assess effects of UAV flights on free-roaming bears. All bears exhibited a stress response to UAV flights as evidenced by elevated heart rates while rarely exhibiting a behavioral response.