The shea tree (Vitellaria paradoxa) is an important tree species in agroforestry systems and bushlands in West Africa and shea nuts are a fundamental resource for rural livelihoods. In this study, sustainability and interactions in agroforestry systems of shea trees were investigated around the Nakpalli village in Northern Ghana. Focus of the study was structure and density of shea tree populations, below-canopy microclimate and co-cultivation of yams (Dioscorea rotundata) under shea tree canopies, and water stress of the trees in the driest season. Shea tree populations are well conserved in this area, but Weibull-distributions of the tree populations and quantification of seedlings showed a lower tree density, especially of seedlings and small trees, in agroforestry fields and fallows, as compared to uncultivated bushlands. This indicates that intensified agroforestry practices might negatively affect the regeneration of shea populations and their long-term regeneration in these agroforestry systems. Co-cultivation of yams in shea canopies allowed production of 11.5 t/ha as compared to 20.8 kg/ha at open field conditions. The lower production may have been caused by an almost 74% reduction of photosynthetically active radiation below canopies, relative to outside the canopies. Shea trees in fields, fallows and bushlands had high predawn leaf water potentials, indicating a low water stress, even in the middle of the dry season. The thriving of shea in the area underlines the importance of conserving this well-adapted indigenous tree in the agroforestry systems and avoiding removal, e.g., by mechanical soil preparation and negative impacts from future climate extremes.