Drought severity has pervasive impacts on honey production via direct impacts on water resources and nectar availability. The current mega-drought in Chile has impacts on water resources and forest vigor, particularly in the Mediterranean and Temperate regions where honey production is concentrated. While honey production plays an important role in the local rural economy and providing pollination services to other agricultural activities, studies of the long-term impacts of the mega-drought on honey production are scarce. Here, we evaluate the impact of climate variability on historical changes in honey production in the Mediterranean (32°S–37°S) and Temperate (37°S–41°S) regions of Chile, using annual honey production records of beekeepers together with national records of honey exports. We also used questionnaires and interviews to evaluate beekeeper perceptions regarding the effects of climate change on honey production and adaptation practices in both regions. Results indicated a declining trend in honey production and exports in the last decade, largely related to changes in precipitation and temperature in both regions. Declines in honey production affected 82% of beekeepers, 80% of whom had employed adaptive measures, and 74% considered that these measures were effective. The drier, warmer Mediterranean region showed more severe declines in precipitation and honey production, which beekeepers reported as a main contributing factor to transhumance from the Mediterranean to the Temperate region. This is the first study to show the effects of drought on honey production in Chile, providing a foundation for future climate change adaptation strategies within apiculture.