Currently, there are several studies related to climate change, carbon sequestration, and floristic composition in different scenarios and land uses. In this context, the objective of this research is: (a) to characterize biodiversity based on ecological indicators and diversity indices and (b) to evaluate carbon sequestration in different components of chakra-type agroforestry systems and secondary tropical humid forests of the Ecuadorian Amazon. For this, temporary sampling plots of 1600 m2 are established on the properties to be investigated. The study found that the structural characteristics and floristic composition vary according to the forest arrangement and the management system. Secondary forests are the most diverse, according to the Shannon (3.49), Simpson (0.96), and Margaleft (9.34) diversity indices, in addition to having the largest carbon stores with 233 (Mg C ha−1), followed by agroforestry systems in association with timber trees (TAFS) and fruit trees (FAFS) with 97.8 and 95.1 (Mg C ha−1) respectively, and cocoa monoculture (CMC) with 90.4 (Mg C ha−1). These results demonstrate the importance of conserving the remnants of tropical forests that still remain, due to the diversity of species, ecosystem services, and the total carbon they contain, as well as the agroforestry systems (AFS), systems analogous to forests, which are gradually becoming important management systems, especially if they are associated with potential species to sequester carbon, such as those documented in this and several other studies that seek solutions to global climate change.