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. The drivers of its compositional variation within and among species remain poorly understood, although this could inform broader and less explored eco-evolutionary theories. 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. Our results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, without identifying a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for the establishment of standards for while highlighting the need for more interdisciplinary and trans-sectoral research.