Tree responses to fertilizer management are complex and are influenced by the interactions between the environment, other organisms, and the combined genetics of composite trees. Increased consumer awareness of the environmental impact of agriculture has stimulated research toward increasing nutrient-use efficiency, improving environmental sustainability, and maximizing quality. Here, we highlight recent advancements and identify knowledge gaps in nutrient dynamics across the soil–rhizosphere–tree continuum for fruit crops. Beneficial soil management practices can enhance nutrient uptake and there has been significant progress in the understanding of how roots, microorganisms, and soil interact to enhance nutrient acquisition in the rhizosphere. Characterizing root architecture, in situ, still remains one of the greatest research challenges in perennial fruit research. However, the last decade has advanced the characterization of root nutrient uptake and transport in plants but studies in tree fruit crops have been limited. Calcium, and its balance relative to other macronutrients, has been a primary focus for mineral nutrient research because of its important contributions to the development of physiological disorders. However, annual elemental redistribution makes these interactions complex. The development of new approaches for measuring nutrient movement in soil and plant systems will be critical for achieving sustainable production of high-quality fruit in the future.