Soil environment strongly contributes to tree growth and development, affecting nutrient and water uptake. Composite woody perennials, like apple, are a combination of two genetically different parts: a rootstock and a scion, and yet, the role of each part on nutrient uptake and distribution under differing soil environments has not been previously studied. We tested how water limitations and elevated soil temperatures, applied to different apple rootstocks and scions, affected mineral nutrient uptake and distribution on young apple trees. Two one-year-old potted apple cultivars were grown in a greenhouse, ‘Honeycrisp’ and ‘Gala,’ combined with four rootstocks: G890, G41, M9, and B9. Belowground abiotic environmental treatments were imposed for 60 days after trees reached approximately 45 cm height. Water limitations reduced aboveground biomass and, to a lesser extent, root biomass. ‘Gala’ and the rootstock G890 showed elevated mineral nutrient uptake compared to ‘Honeycrisp’ and the other rootstock genotypes. Additionally, G890 showed a greater plasticity for both biomass and mineral nutrient accumulation. Elevated soil temperatures increased the ratios of K:Ca, N:Ca, Mg:Ca, and (N + K + Mg):Ca in leaf tissue of rootstock G41 and ‘Honeycrisp’. These findings highlight the importance of the use of scion and rootstock genotypes that are adapted to specific soil environments to ensure optimal nutrient uptake.