‘Candidatus Liberibacter asiaticus’ (CLas), an alpha-proteobacteria associated with huanglongbing (HLB) and transmitted by Diaphorina citri is the most devastating pathogen of citrus. After initial infection, CLas quickly colonizes the root system before visible canopy symptoms develop. Understanding how CLas moves within the plant and local and systemic effects of CLas on different tissues is fundamental to improve HLB management. Using split root rhizotrons and one-side graft inoculation below the trunk split in late summer was used to study the role of root infection on disease development. Root dieback increased on both halves of the root system in as little as 6 weeks, even though CLas infection remained isolated in the inoculated half of the root system through late summer and fall root flush. More root growth occurred in the non-infected half of the root system of HLB-affected trees during late summer and fall root flush compared to healthy trees and live root length after each seasonal flush. Increased root dieback removed this gain by the next root flush. The first detection of CLas in canopies occurred in the spring flush, with 6 canopies CLas-infected at the end of the experiment (11 months). The results showed that movement of CLas from infected root systems is linked to season, where it can move up and around the trunk after the spring flush; however, systemic effects on the root system are not dependent on CLas movement.