Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.