Improving nutrient uptake and tree health play an important role in managing Huanglongbing (HLB)-affected citrus trees in Florida. A greenhouse experiment was conducted to evaluate the effect of increasing rates of manganese (Mn) on growth and development of sweet orange [Citrus sinensis (L.) Osbeck] trees at the University of Florida’s Institute of Food and Agricultural Sciences (UF/IFAS) Citrus Research and Education Center in Lake Alfred, FL. Half the trees were graft-inoculated with the HLB pathogen and the remainder were used as the HLB-free (non HLB) control trees. Four rates of Mn (0.0 kg·ha−1 Mn (Control), 5.6 kg·ha−1 Mn (1x—standard rate), 11.2 kg·ha−1 Mn (2x—standard rate), and 22.4 kg·ha−1 Mn (4x—standard rate) were split applied quarterly to both sets of the trees in a completely randomized design. There were seven single tree replicates for each treatment. Response variables measured were trunk diameter, tree height, leaf Mn concentration, plus above- and belowground biomass. The accumulated Mn in leaf tissues significantly increased trunk diameter but did not affect tree height for both HLB-affected and non-HLB trees, the 2x rate had the maximum value for trunk diameter relative to the 4x rate. This study established a positive correlation between soil available Mn with Fe and Cu, but negative correlation with B and Zn. A strong correlation of −0.76, −0.69, and 0.65 was observed between soil Mn and B, Zn, and Cu, respectively, as compared with 0.49 with Mn and Fe. Among HLB-affected trees, the 2x rate gave the most belowground dry matter, which was 3% greater than the control and 5% greater than 4x. Aboveground dry matter had at least 30% more biomass than belowground matter among all treatments within HLB-affected trees. For small and medium roots, Mn accumulation increased with Mn application until 2x rate and decreased thereafter for HLB-affected trees. The results from our study showed an Mn rate of 8.9–11.5 kg·ha−1 Mn, as the optimum Mn level for young ‘Valencia’ HLB-affected trees in Florida.