Agroforestry systems usually include a high density and diversity of shade trees. Such systems often have a large diversity of fauna and flora and provide local and regional ecosystem services. Shade trees are, however, being removed to increase crop production in many tropical regions. There is little knowledge on the effect of shade trees on crop production in the context of trade-offs with other management practices. We therefore compared the benefits of exotic versus native shade trees on coffee production. We evaluated the importance of shade tree management for crop production in the context of management practices. Management practices included fertilization, liming, coffee pruning, weeding, and irrigation in 113 coffee agroforests in Kodagu, India, over a wide range of shade tree density, tree species diversity, and shade cover. We studied, in particular, Grevillea and non-Grevillea shade trees, the latter including mostly native tree species. Results show that a rise of 100 non-Grevillea shade tree per hectare increased production of berries by 5.6 % and larger beans by 6.25 %. Irrigation and liming increased berry production respectively by 16 and 20 %. These management interventions are likely to offset the relatively small negative effect of reducing shade density of non-Grevillea trees on coffee production. Recommendations based on an understanding of shade tree management alone can be misleading with regard to crop production.