The shea tree (Vitellaria paradoxa C.F. Gaertn.) is an important tree species in agroforestry systems in West Africa and shea nuts constitute a fundamental resource for rural livelihoods in this area. This study investigated the sustainability and interactions in agroforestry systems of shea trees around the village Nakpalli in Northern Ghana. The focus of the study was the population structures and densities of shea trees on different land types, below-canopy microclimate and co-cultivation of yams (Dioscorea rotundata (Poir.) J. Miége) under shea tree canopies, and water stress of the trees in the driest season. Shea tree populations are overall well-conserved in this area, but Weibull-distributions of the tree populations and quantification of seedlings showed a lower tree density in both cultivated and fallowed lands, as compared to undisturbed bushlands. Although farmers may deliberately manage the density of larger trees, the low densities of seedlings and saplings indicate that intensified management practices, including shortened fallow periods and intentional clearing of land by fire before sowing, might negatively affect the long-term regeneration of the shea trees. Co-cultivation of yams below shea tree canopies allowed production of 11.5 t/ha as compared to 20.8 t/ha at open field conditions. The lower yields may have been caused by an almost 74% reduction of photosynthetically active radiation below canopies, relative to outside the canopies. Shea trees in the fields, fallows and bushlands had close-to-zero predawn leaf water potentials, indicating low water stress, even in the middle of the dry season. Thus, shea trees are both well-adapted and highly valued in this area, which underlines the importance of conserving this indigenous tree species in the agroforestry systems of northern Ghana.