Huanglongbing (HLB) is a devastating disease of citrus that is found in most citrus production areas around the world. The bacterium associated with HLB resides in and damages the phloem, restricting the movement of photosynthates throughout the plant and leading to tree decline. Considerable root loss can be observed in affected trees even when few disease symptoms are visible aboveground. Root traits can substantially influence tree performance and use of superior rootstocks is one strategy to manage tree health and reduce production losses in a disease-endemic environment. Citrus rootstocks are typically propagated by seed, but due to the increased demand for some of the best-performing cultivars, propagation by other methods is being used to overcome seed shortages. In this research, differences in root architecture and root growth of six different rootstocks propagated by seed, cuttings, and tissue culture, and their influence on the grafted ‘Valencia’ (Citrus sinensis) scion were investigated. A field trial was established in southwest Florida in 2017. Trees were evaluated for their performance during the first 2 years after planting and a subset of trees was excavated for detailed analysis of root architectures and biomass distribution. Significant differences among propagation methods were found for the rootstock trunk diameter and the lateral (structural) root length, which were largest in seed-propagated rootstocks. Most of the other horticultural and root architectural traits were not significantly influenced by the rootstock-propagation method; however, many of the measured variables were significantly influenced by the rootstock cultivar regardless of the propagation method. The results showed that rootstocks propagated by cuttings and tissue culture were similar to seed-propagated rootstocks in their influence on the grafted tree during the early years of growth in the field.