The rootstock plays a large role in modern citrus production because of its influence on tolerance to adverse abiotic and biotic soil-borne stresses, and on the general horticultural characteristics of the grafted scion. In recent years, rootstock has received increased attention as a management strategy to alleviate the devastating effects of the bacterial disease huanglongbing (HLB), also known as “citrus greening.” In commercial citrus nursery production, rootstocks are typically propagated by seed. Because of the increased demand for HLB-tolerant rootstocks, seed supply is often inadequate for the most popular cultivars. Cuttings and tissue culture (TC) propagation are alternative methods to supply adequate quantities of genetically identical rootstocks to be used as liners for grafting. However, there are concerns among nursery owners and citrus growers regarding the possible inferiority of rootstocks that are not propagated by seed. This study investigates the influence of rootstock propagation method on traits of sweet orange trees grafted on four commercially important rootstock cultivars during the nursery stage and during the first year of growth in a commercial citrus orchard. Several of the measured traits during the nursery stage, including rootstock sprouting, grafted tree growth, and root mass distribution were significantly influenced by the rootstock propagation method, but traits were also influenced by the rootstock cultivar. Our results also suggest that for tissue culture-propagated plants, differences in the starting material and the culturing method can affect the grafted tree behavior. Except for canopy spread and scion to rootstock trunk diameter ratio, tree growth during the orchard stage was determined by the combination of propagation method and rootstock, rather than by propagation method alone.