Huanglongbing {HLB [Candidatus Liberibacter asiaticus (C Las)]} has been one of the biggest challenges in citrus (Citrus sp.) production in Florida and wherever it is present. HLB-affected trees show significant shoot and root dieback, fruit drop, and reduction in yield. Currently, there is no cure for HLB, and there is no commercial HLB-resistant germplasm. Nonetheless, intensive nutrient management has been promising for citrus growers. The nutrient requirement of HLB-affected trees seems to be greater than that of healthy citrus trees. By understanding the nutrient uptake potential of rootstocks, fertilizer programs can be customized accordingly to enhance the performance of a rootstock in existing groves. Moreover, a reduction in the application of nutrients is possible by planting rootstocks with a high nutrient absorption capacity. Use of rootstocks with good nutrient uptake efficiency can take some burden off the growers who are intensively managing HLB-affected citrus groves. Therefore, the objective of this study was to evaluate and understand the nutrient uptake potential of the citrus rootstocks. To achieve this objective, a 100% hydroponic greenhouse study was conducted with six rootstocks with a range of tolerance to HLB. Several physiological and molecular tools were applied to evaluate the rootstocks for their nutrient uptake potential. A+Volk × O-19 (HLB-tolerant) rootstock had greater nutrient uptake efficiency, whereas US-896 (HLB-susceptible) had lesser nutrient uptake efficiency. Swingle, one of the most popular pre-HLB rootstocks, had poor zinc uptake and the least expression of ZINC TRANSPORTER, suggesting that zinc applications should be emphasized in Swingle plantings. US-896 rootstock expressed the least level of nutrient transporter genes, such as IRON TRANSPORTER. UFR-4 (a good performer under HLB conditions) had a large root biomass, but the uptake efficiency for nutrients was poor, suggesting that the nutrient uptake potential is a complex process that is not solely dependent on root biomass. This study is unique because it is one of the first citrus studies to report nutrient uptake efficiency and the potential of rootstocks. The information presented can be used to improve performance or select better-performing rootstocks under HLB conditions.