The combined use of Individual Protective Covers (IPCs) and oxytetracycline (OTC) trunk injection offers a promising strategy for managing huanglongbing (HLB) in young citrus trees by reducing environmental stress and preventing Candidatus Liberibacter asiaticus (CLas) inoculation. This study evaluated whether young citrus trees that were grown without IPCs for the first two years after planting and severely affected by HLB can be rehabilitated by OTC injections, and whether IPCs provide additional benefits beyond OTC alone. ‘Valencia’ sweet orange trees on US-812 and US-942 rootstocks, were organized in a randomized complete block design with three treatments: 1) no injection no IPC, 2) OTC injection no IPC, and 3) OTC injection IPC. Each treatment-rootstock combination consisted of 14 single-tree replications. Trunk injections were performed annually for two years (2023-2024) using Chemjet tree injectors, with solutions delivered into the rootstock. Comprehensive data were collected on the yield, juice quality, bacterial titers, disease state, flushing patterns, and psyllid infestation. No significant differences were observed between the rootstocks except for the juice quality, which was better in combination with US-812. OTC-injected trees consistently exhibited higher yields and improved juice quality, with no additional benefits from IPCs. A significant decrease in CLas titers was noted starting three months post-injection. Injected trees under IPCs had fewer HLB symptoms in the second year, and injected trees exhibited a significant increase in canopy density compared with non-injected trees. Trees with IPCs flushed less frequently during summer and winter than trees without IPCs. The psyllid infestation rate was the same in injected and non-injected trees, indicating that OTC treatment does not affect host attractiveness. These findings highlight the potential of OTC trunk injection to rehabilitate young HLB-affected citrus trees and enhance tree productivity. The longer-term role of IPCs in young tree rehabilitation is still under investigation.