Silvopastoral systems (SPS) have been widely implemented in the Colombian Amazon region to improve pastures involving a greater diversity of species, soil tillage, fertilization, and higher stocking rate, which can induce changes in soil properties and functions. This study aimed to evaluate soil chemical properties and carbon sequestration changes due to the transition from traditional pastures to silvopastoral systems. The study was conducted in the Colombian Amazon region, specifically in La Montañita and El Doncello Counties, in Caquetá, the second most important hotspot of deforestation in the entire Amazon basin. In each study site, we established a chronosequence consisting of three areas following the typical land‐use change at the region: (i) native vegetation, (ii) traditional pasture, and (iii) silvopastoral system. We found that agricultural practices involving liming and tillage, performed under the silvopastoral management, contributed to reducing soil active acidity and exchangeable acidity with soil pH increasing from 3.8 to 4.3 and H++Al3+ decreasing from 5.8 to 2.3 cmolc kg−1. These alterations favored increases in Ca2+ and Mg2+ contents mainly, increasing the base saturation from 17% in traditional pastures to 55% under silvopastoral systems. The synergic effect of the mix of grasses and trees under silvopastoral management improved soil micronutrient contents and modified soil C stocks in 20–30 cm layer. A rate of soil C accretion of 0.26 Mg ha−1 yr−1 for the 0–30 cm detected in silvopastoral systems suggests that its implementation could be a promising tool for C sequestration in tropical regions, capable of restoring soil functioning of degraded areas.