<p>Cacao (<i>Theobroma cacao</i> L.), the key crop in global chocolate production, has been propagated by somatic embryogenesis (SE) for decades. However, challenges such as recalcitrance and genotype dependency still limit its efficiency. To better understand the cellular and structural basis of SE and plant regeneration in this species, we evaluated the effects of different cytokinins on SE induction from staminodes of three cacao genotypes (‘752’, ‘754’, and ‘755’), and characterized the morphoanatomical and histochemical features of the resulting callus types and somatic embryos. Staminodes were excised from floral buds and cultured on a modified callus induction medium supplemented with kinetin or <i>meta</i>-Topolin at 0, 0.5, or 1.0 mg L^− 1. Genotype significantly influenced embryogenic responsiveness, and the basal region of the explants showed greater response, although no specific anatomical traits were associated with this pattern. Embryogenic calli were markedly darkened, a typical feature in cacao associated with phenolic accumulation, and this response occurred independently of cytokinin supplementation. The cytokinins tested did not enhance the embryogenic response. Morphoanatomical analysis revealed a high degree of heterogeneity in the callus masses, with nodular and granular types frequently co-occurring. These were characterized by clusters of embryogenic cells interspersed with vacuoles, non-embryogenic cells, both types being rich in phenolic compounds. Histological evidence indicated both multicellular (via meristematic clumps) and unicellular (via proembryos) origins of somatic embryos. Advanced-stage somatic embryos lacked storage reserves and often exhibited developmental abnormalities. These findings contribute to the understanding of cacao SE and regeneration and provide a foundation for future studies aiming to elucidate the histochemical and anatomical traits associated with embryogenic competence.</p>