Honey farming is a young industry in Colombia, where it is gaining relevance as a source of jobs and food security, especially in post-conflict low-income communities that place bee colonies in native forests. Previous studies on the palynological composition of this honey are insufficient and the role of native plants for the production of honey is therefore unknown. Here we present a palynological analysis of honey produced by two bee species, the introduced Apis mellifera and the native Melipona eburnea, both commonly used by low-income communities in the eastern region of the Department of Antioquia, in the Central Cordillera of Colombia. We analyzed species richness and diversity of pollen, characterized some life history traits of those species preferred by bees, and estimated the interaction web between the bee and selected plant species. The overlap between the two species was very small. We found that the source of nectar for A. mellifera were plants with different growth habits, both native and introduced. Instead, M. eburnea used mostly native tree and shrub species, at a constant height level. Our results suggest that setting bee colonies of A. mellifera close to those of M. eburnea may not result in competition between them. However, it is key to evaluate whether this pattern is the same using other sources of food, such as pollen, or in other geographic regions.