There is a high diversity of bees in the tropics, including honey bees and stingless bees, which are the main sources for honey and other ecosystem services. In Indonesia, beekeeping practices have been developed for centuries, and they have been part of many cultural practices in many traditional communities. The objective of this research was to study the beekeeping status and managed bee diversity in Indonesia and to investigate beekeepers’ perspectives on the factors and obstacles related to beekeeping. Direct interview and online interview were conducted to gain data on bees and beekeepers. In total, 272 beekeepers were interviewed across 25 provinces. Samplings of honey bees and stingless bees were also done during direct interviews for further identification and, when possible, pollen identification. All data and specimens were then sent to IPB Bogor for compilation and identification. We recorded 22 species of bees, including 3 species of honey bees and 19 species of stingless bees, that are reared by Indonesian beekeepers, with Apis cerana and Tetragonula laeviceps as the most common species. Our research also found that the majority of beekeepers fall into the category of the younger generation (30–39 years old) with educational background mostly from senior high school. Based on the beekeepers’ perspectives, there are several obstacles to beekeeping, especially the occurrence of death of bee foragers attributed to climate, food source, and pesticides. In conclusion, there is a need to develop a strategy for beekeeping and bee conservation in Indonesia, especially for adaptation and mitigation from environmental changes with a particular focus on climate and land-use change.