The identification of the factors that cause changes in agroecosystems and the services they provide is essential to design management that minimizes negative impacts on the environment. In this sense, the objective of this research was to characterize some structural indices and the carbon sequestration potential under different land uses in the Ecuadorian Amazon region. In each selected land use, we collected disturbed an undisturbed soil samples within depths from 0-10 and 10-30 cm. From these samples were evaluated some structural indexes such as the bulk density (BD), saturated hydraulic conductivity (K_sat), total porosity. (Tp), aeration porosity (Ap), retention porosity (Rp) and total organic carbon (TOC). The results showed significant differences by treatment and depth, obtaining the best physical condition in the Forest and in some uses of grass with trees. Regardless of land use, the structural conditions evaluated through the structural indexes exhibited better results in the surface horizon, which is strongly associated with the content of organic matter. It is shown that the reduction of greenhouse gas emissions (CO₂) is associated with the increase and protection of organic matter with agroforestry systems.