Anthropogenic land cover change is directly responsible for the deforestation and degradation of tropical forests. In this context, assessing soil organic carbon (SOC) stocks is key to understanding the impact of anthropogenic activities on SOC so that we can implement management practices that effectively reduce emissions or promote carbon sequestration. Our objective was to assess the effect of land-use change on the dynamics and distribution of SOC in three systems (agriculture, pasture and agroforestry) after 40 years of deforestation in a tropical dry forest in the central–eastern region of Honduras. For this purpose, the bulk density, percentage of coarse fragments (>2 mm) and soil organic carbon content were determined at three depths (0.00–0.10 m, 0.10–0.20 m and 0.20–0.30 m). The results showed an increase in bulk density for all new uses, although soil compaction had not yet occurred. In terms of total soil organic carbon (TOC) stocks, deforestation caused a decrease from 17% to 48% in agricultural and agroforestry soils, respectively; on the other hand, grasslands did not show significant differences compared to tropical dry forest, suggesting that they have a high potential as carbon sinks in deforested tropical areas. However, this did not imply a better state of the system, as the greatest increases in bulk density were found in pastures.