In understudied regions of the world, beekeeper records can provide valuable insights into changes in pollinator population trends. We conducted a questionnaire survey of 116 beekeepers in a mountainous area of Western Nepal, where the native honeybee Apis cerana cerana is kept as a managed bee. We complemented the survey with field data on insect–crop visitation, a household income survey, and an interview with a local lead beekeeper. In total, 76% of beekeepers reported declines in honeybees, while 86% and 78% reported declines in honey yield and number of beehives, respectively. Honey yield per hive fell by 50% between 2012 and 2022, whilst the number of occupied hives decreased by 44%. Beekeepers ranked climate change and declining flower abundance as the most important drivers of the decline. This raises concern for the future food and economic security of this region, where honey sales contribute to 16% of total household income, and where Apis cerana cerana plays a major role in crop pollination, contributing more than 50% of all flower visits to apple, cucumber, and pumpkin. To mitigate further declines, we promote native habitat and wildflower preservation, and using well-insulated log hives to buffer bees against the increasingly extreme temperature fluctuations.