Huanglongbing (HLB), an important citrus disease, causes many physiological and anatomical changes such as phloem dysfunction, imbalance in carbohydrate partitioning, decrease in leaf chlorophyll, and nutritional imbalances in the affected trees, ultimately resulting in tree decline. In Florida, HLB is associated with phloem-limited bacteria Candidatus Liberibacter asiaticus (CLas), and it is vectored by the Asian citrus psyllid (Diaphorina citri). No cure for HLB has been found, and most of the HLB management efforts have been focused on vector control or exclusion, improved nutrient management, and the use of HLB-tolerant rootstocks. Individual protective covers (IPCs) are a type of psyllid exclusion tool that is increasingly used by growers for HLB management of newly planted citrus trees. However, no studies have evaluated their influence on citrus tree physiology. This study investigated the effect of IPCs and different rates of insecticides on CLas infection and different physiological attributes, including soluble (glucose, fructose, and sucrose) and nonsoluble (starch) carbohydrates, leaf chlorophyll, and leaf macronutrients and micronutrients over 2.5 years of field growth. The treatments (tree cover and insecticides rate) were applied in newly planted ‘Valencia’ sweet orange (Citrus sinensis) trees grafted on ‘Cleopatra’ (C. reticulata) rootstock. The IPCs prevented CLas transmission and accumulation of foliar starch, sucrose, and glucose commonly associated with HLB. IPC-covered trees had more leaf chlorophyll-a and chlorophyll-b than noncovered trees and more leaf nitrogen (N) and zinc (Zn). Our findings suggest that IPCs effectively prevent CLas infection and maintain the physiological health of young citrus trees under heavy HLB pressure. Therefore, IPCs are recommended as an important component of integrated pest management for this devastating disease.