Twelve cacao (Theobroma cacao) clones propagated by grafting and orthotropic rooted cuttings of somatic embryo-derived plants were grown on an Ultisol soil at Corozal, Puerto Rico, and evaluated for 6 years of production under intensive management. Year, variety, year × variety, and propagation treatment × variety interactions indicated significant effects for dry bean yield, number of pods produced, pod index, plant height, and stem diameter. Propagation treatments had a significant effect on dry bean yield and pod index but not on number of pods produced. Average yield across varieties for both propagation treatments was 2087.9 kg·ha−1 per year of dry beans. There was a highly significant variety effect. ‘UF-668’ was the top yielder averaging 2536.7 kg·ha−1 per year of dry beans; however, this yield was not significantly different from the average yield of varieties ‘TARS-30’, ‘TARS-1’, ‘TARS-13’, ‘TARS-14’, and ‘TARS-2’, which averaged 2427.0 kg·ha−1 per year. Except for ‘UF-668’, the TARS varieties were released in 2009 as high-yielding selections. Propagation treatments had a significant effect on dry bean yield. Dry bean yield of varieties propagated by grafting was 7% higher (2166.7 kg·ha−1 per year) than those propagated by orthotropic rooted cuttings of somatic embryo-derived plants (2009.2 kg·ha−1 per year). This yield difference could not be attributed to grafted plants being more vigorous nor by differences in root architecture. The lowest pod index value in both propagation treatments was obtained by ‘UF-668’; however, pod index for this variety did not differ significantly from values for ‘TARS-2’ and ‘TARS-23’ in grafted plants and from ‘TARS-2’, ‘TARS-23’, and ‘TARS-1’ in plants propagated by orthotropic rooted cuttings of somatic embryo-derived plants. With few exceptions, flavor characteristics were not significantly affected by propagation treatments. Although there were significant differences between plant propagation treatments for some of the variables measured in this study, these were not of a magnitude that would preclude the use of somatic embryogenesis as a viable propagation system for cacao.