Bees flying through natural landscapes encounter physical challenges, such as wind and cluttered vegetation. The influence of these factors on the flight performance of bees 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 fly within (through open corridors, without maneuvering) or above. We examined how obstacle field height, wind presence and direction (headwinds or tailwinds) affected altitude, ground speed, and side-to-side casting (lateral excursions) of bees. 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 typically, but not always, increased their altitudes to fly over the obstacles. Bees that flew above the obstacle fields exhibited 40% faster ground speeds and 36% larger lateral excursions than bees that flew within the obstacle fields, likely due to the visual feedback from obstacles and narrow space available within the obstacle field. Wind had a strong effect on ground speed and lateral excursions, but not altitude. Bees flew 12-19% faster in tailwinds than in the other wind conditions, but their lateral excursions were 19% larger in any wind, regardless of its direction, than in still air. Our results show that bees flying through complex environments display flexible flight behaviors (e.g., flying above versus within obstacles), which affect flight performance. Similar choices in natural landscapes could have broad implications for foraging efficiency, pollination, and mortality in wild bees.