In the sub-humid parts of East Africa, high population density and pressure on land have led farmers to integrate multipurpose trees on farm. Although mixing trees and crops generates numerous benefits (e.g., fuelwood, timber), it often reduces crop yields. Whereas the effects of mature trees on crops are well studied in semi-arid parklands, there are only few studies for the sub-humid environment. The effects of mature Alnus acuminata (Kunth) and Markhamia lutea (Seem.) on crops were studied on-farm for four seasons in the sub-humid environment of northern Rwanda. Five sampling points for A. acuminata and M. lutea were: (i) 1 m from tree trunk without maize, (ii) 3 m from tree trunk without maize, (iii) 1 m from tree trunk with maize, (iv) 3 m from tree trunk with maize and (v) sole maize away from any tree. Nutrient availability and uptake, soil water, air temperature, solar radiation, crop growth and yields were measured. The APSIM-maize module was used to assess the sensitivity of maize yields to changes in these variables. Nutrients availability was higher under A. acuminata compared with M. lutea, because of higher litter fall but maize nutrient uptake increased only under A. acuminata 3 m from tree trunk during a wetter season. None of tree species affected water availability for maize in the topsoil. Photosynthetically active radiation (PAR), total solar radiation and day air temperature were reduced by both tree species. Maize crop at 1 m and 3 m from the tree trunk was shorter in height but had the same number and size of leaves when compared to sole maize plots. Crop yield was generally reduced more at 1 m than at 3 m from the tree trunk. A positive interaction between A. acuminata and maize was only apparent at 3 m from the tree in one of the four seasons following higher litter fall, suggesting that the negative effect of shade was offset by extra N input during that season. In a modelled scenario under low N fertilization, larger N input from trees could compensate for yield loss caused by reduction in radiation and temperature in about 60% of the seasons. Our findings suggest that adequate pruning and high leaf litter recycling can reduce the negative effect of shade in low intensity farming systems.