Bees flying through natural landscapes frequently encounter physical challenges, such as wind and cluttered vegetation, but the influence of these factors on flight performance remains unknown. We analyzed 548 videos of wild-caught honeybees (Apis mellifera) flying through an enclosure containing a field of vertical obstacles that bees could choose to fly within (through open corridors, without maneuvering) or above. We varied obstacle field height and wind condition (still, headwinds or tailwinds), and examined how these factors affected bees' flight altitude, ground speed, and side-to-side casting motions (lateral excursions). When obstacle fields were short, bees flew at altitudes near the midpoint between the tunnel floor and ceiling. When obstacle fields approached or exceeded this midpoint, bees tended to increase their altitude, but they did not always avoid flying through obstacles, despite having the freedom to do so. Bees that flew above the obstacles exhibited 40% faster ground speeds and 36% larger lateral excursions than bees that flew within the obstacle fields. Wind did not affect flight altitude, but bees flew 12-19% faster in tailwinds, and their lateral excursions were 19% larger when flying in headwinds or tailwinds, as compared to still air. Our results show that bees flying through complex environments display flexibility in their route choices (i.e., flying above obstacles in some trials and through them in others), which affects their overall flight performance. Similar choices in natural landscapes could have broad implications for foraging efficiency, pollination, and mortality in wild bees.