The bacterial disease Huanglongbing (HLB) has drastically reduced citrus production in Florida. Nutrients play an important role in plant defense mechanisms and new approaches to manage the disease with balanced nutrition are emerging. Nutrients like nitrogen (N), calcium (Ca), and magnesium (Mg) could extend the productive life of affected trees, although interactions among these nutrients in HLB-affected citrus trees are still unclear. A 2-year study was established in Florida to determine the response of HLB-affected trees to applications of N, Ca, and Mg. The study was conducted with ‘Valencia’ trees (Citrus sinensis L. Osbeck) on Swingle citrumelo (Citrus paradisi Macf. × Poncirus trifoliata L. Raf.) rootstock on a Candler sand. Applications of N at 168, 224 (recommended rate), and 280 kg⋅ha−1 N were used as the main plots. Split-plots consisted of a grower standard treatment receiving only basal Ca (51 kg⋅ha−1) and Mg (56 kg⋅ha−1); supplemental Ca (total Ca inputs: 96 kg⋅ha−1) only; supplemental Mg (total Mg inputs: 101 kg⋅ha−1) only; and supplemental Ca (total Ca inputs: 73.5 kg⋅ha−1) and Mg (total Mg inputs: 78.5 kg⋅ha−1). The following variables were measured: tree size, fruit yield, and juice quality. Although some differences in tree growth among treatments were statistically significant (e.g., greater canopy volume with Mg fertilization at 168 kg⋅ha−1 N), there was no clear and consistent effect of plant nutrition on these variables. Fruit yield was higher with Ca and Mg relative to the grower standard at the lowest N rate in 2020, and there were no other statistically significant differences among treatments. Juice acidity was significantly higher with Mg fertilization relative to other treatments in 2019. As N rates had no significant effect in this study, unlike secondary macronutrients, N rates could potentially be reduced to 168 kg N⋅ha−1 in HLB-affected citrus without affecting vegetative growth, fruit yield, and juice quality. However, this will require optimizing the supply of secondary macronutrients and all other nutrients to develop a balanced nutritional program. Ultimately, the effects of N, Ca, and Mg obtained in this 2-year study should be confirmed with longer-term studies conducted at multiple sites.