Animal-pollination is crucial in the reproduction of many crops grown in the tropics, including the self-incompatible Robusta coffee. Coffea canephora Pierre ex A. Froehner. is indigenous to the Congo basin where it is naturally growing in the rainforest understorey. Coffee cultivation mainly occurs in either unshaded monocultures or in agroforestry systems. Here we used pan traps to survey the Diptera (true flies) and Hymenoptera (bees) communities as the putative coffee pollinating organisms in the Yangambi region in DR Congo, and we assessed the comparative benefits of a coffee agroforestry system and coffee monoculture to the coffee pollinator community. To assess the pollinator conservation potential of the agroforestry system, we also compared its Diptera and Hymenoptera communities with natural rainforest as a benchmark. Natural rainforest harboured a higher number of individuals, as well as a higher number of species than both agroforestry and coffee monoculture systems, with no differences between the latter two land-uses. Furthermore, we observed different responses in species richness and diversity to land-use between Diptera and Hymenoptera. Our analyses further showed a high species dissimilarity between natural rainforest and the two cultivation systems, without significant differences between the latter. Specifically, the community composition of the agroforestry and coffee monoculture systems were totally different, rather than a subset of the community composition of the natural rainforest. Our study indicates that rehabilitation of agricultural land through intercropping fruit trees may not always enhance pollinator communities and that the studied agroforestry system falls short of matching the bee and fly conservation potential of natural rainforests.