Natural habitat degradation often involves the reduction or disappearance of bee species. In Africa, stingless bees are hunted for honey, which is used as food, for medicinal purposes, and for traditional rituals. Severe habitat degradation due to human settlement is hypothesized to have a negative impact on the species diversity of the African stingless bee species. In this paper, we assess the impact of habitat degradation on the diversity of five stingless bee species across different habitats in the tropical rainforest of Kenya (indigenous forest, mixed indigenous forest) and its neighbouring landscape (grassland, village) in western Kenya. The species fauna, nest occurrence, and species diversity of the stingless bee species varied across the different habitats. The number of nesting habitats of the meliponine species varied between habitats in the tropical rainforest. Meliponula ferruginea (reddish brown) nested in five habitats, while Meliponula bocandei and Meliponula ferruginea (black) nested only in two habitat types. The species richness decreased within the different types of habitats and the indigenous and mixed indigenous forest contained more species than other habitats. The fauna composition in both homesteads was exclusively similar, while the indigenous and mixed indigenous forests were mostly similar. Similarity in habitat preferences for nesting was revealed between M. bocandei vs Plebeina hildebrandti and M. ferruginea (reddish brown) vs Hypotrigona gribodoi. The natural native indigenous forest had the most diverse community compared to the degraded habitats. There are taxon-specific responses to habitat change; and in our study, there is clear value in conserving the native indigenous forest.