<p><strong>Background:</strong> In Colombia, most traditional cocoa crops are developed under agroforestry systems (SAF), associating shrubs and trees that provide shade for cocoa. They generate additional economic income and various ecosystem services. <strong>Objective:</strong> To characterize agroforestry systems with cocoa in three municipalities in eastern Boyacá (Miraflores, Berbeo, and Páez) belonging to the province of Lengupá. <strong>Methodology:</strong> A semi-structured interview was applied in 15 selected farms to learn about socioeconomic aspects, agronomic management of cocoa, and the use and management of trees. The botanical and structural composition and the Simpson (S), Shannon-Weaver (H´), and Jaccard (J) plant diversity indices were determined. <strong>Results:</strong> Cocoa producers in that region develop smallholder production under agroforestry systems with irregular tree species distribution, which are used for wood, firewood, shade, and food. At the regional level, 189 forest individuals accompanying cocoa were found, grouped into 18 families, 17 genera, and 28 species. The municipality of Berbeo presented the highest abundance (73 individuals), followed by Miraflores (67) and finally, Páez (49). In Berbeo, the species with a high importance value index (IVI) were <em>Ceiba pentandra</em> and <em>Cedrela odorata</em> (35 and 33, respectively), in Miraflores <em>Trichant<strong>h</strong>era gigantea </em>and <em>Persea americana</em> (44 and 42) and, in Páez <em>Cedrela odorata</em> (104). <strong>Implications:</strong> The selective felling of forests in SAF with cocoa, which intensifies the production of wood, has favored the loss of diversity; Therefore, the floristic composition studies serve as a basis to identify other potential forest species for the establishment of SAF to promote the diversification of the productive system and contribute to its resilience and sustainability. <strong>Conclusion:</strong> The agroforestry systems with cocoa in three municipalities in eastern Boyacá presented a differential composition and diversity, marked by a lower diversity in the municipality of Páez, where the species <em>C. odorata</em> had greater representation, related to the affinity of farmers for timber species of commercial interest.</p>