The fate of foliar and ground-applied essential nutrients is the least studied topic under citrus greening or Huanglongbing (HLB)-affected citrus, which is inherently suffering from severe root decline because of HLB-associated problems. The objective of this study was to evaluate if ground-applied coupled with foliar spray of essential nutrients can reverse the decline in tree growth and understand the fate of the nutrients in the soil-root-tree interfaces. The treatments were arranged in a split-split plot design in which nitrogen (N) was ground-applied in 20 splits biweekly and Mn, Zn, and B were foliar and /or ground-applied in three splits following the spring, summer, and late summer flush seasons. Soil nutrients in three depths (0–15, 15–30, and 30–45 cm), root, and leaf nutrient concentrations of the essential nutrients, leaf area index (LAI), and tree canopy volume (TCV) data were studied twice (spring and summer) for two years. A significantly higher soil NH4-N and NO3-N concentrations were detected in the topsoil depth than the two lower soil depths (15–30 and 30–45 cm) indicating lesser nutrient leaching as trees received moderate (224 kg ha−1) N rate. Except for soil zinc (Zn) concentration, all the nutrient concentrations were significantly higher in the topsoil (0–15 cm), compared with two lower soil depths indicating that Zn was intricate by changes in soil environmental conditions, root acquisition, and/or leaching to lower soil depth. Leaf N concentration significantly increased over time following seasonal environmental fluctuations, tree growth, and development. Thus, leaf N concentration remained above the optimum nutrient range implying lower N requirement under irrigation scheduling with SmartIrrigation, an App used to determine the daily irrigation duration to meet tree water requirement and split fertigation techniques. Root Manganese (Mn) and Zn concentrations were significantly higher in the root tissues of the treated than the control trees and translocated to the leaves accordingly. Meanwhile, a significantly higher LAI for trees budded on Swingle (Swc) rootstock however, larger TCV for trees budded on Volkameriana (Volk) rootstocks. The trees had significantly larger TCV when the trees received a moderate N rate during early study years and under foliar 9 kg ha−1 coupled with the ground 9 kg ha−1 Mn and Zn treatments during the late study years. Therefore, split ground application of 224 kg ha−1 of N, foliar applied 9 kg ha−1 coupled with ground-applied 9 kg ha−1 Mn and Zn were the suggested rates to sustain the essential leaf nutrient concentration within the optimum ranges and improve the deterioration of vegetative growth associated with HLB-induced problems of citrus trees.