Grafting in tomato has been investigated mainly in small-scale experiments, demonstrating morphological, physiological, and metabolic changes in the scion mediated by the rootstock. By grafting a scion onto different rootstocks, scion salt tolerance can be altered and improved, leading to enhanced plant growth, fruit yield, and fruit quality. Increased salt tolerance, manifested as improved growth or physiological performance of the grafted tomatoes, is due to interactions between the scion and rootstock. However, no comprehensive investigation has been performed to determine how the metabolic response of plant leaves under sub-optimal conditions is mediated by rootstock biodiversity or how rootstock-mediated leaf metabolism is associated with plant yield traits.