Pastures are of central importance in food production and provide multiple ecosystem services. The objective of this paper was to determine whether the intensification of pasture-based animal production systems, through practices such as fertilization and improved pasture species, has a higher capacity in the short-term (five years) to sequester carbon in the soil compared to (1) natural grassland without anthropogenic interactions, (2) natural grassland fertilized and overseeded with exotic species, and (3) annual pastures with frequent soil disturbance. The study assessed the organic carbon stock (OCS), total organic carbon (TOC), particle size, porosity, and density at different soil strata, as well as the root system and forage production. Forage dry matter (DM) production varied significantly with means ranging from 6615 to 13,000 kg ha–1 year–1 for natural grassland (NG) and permanent pasture (PP), respectively. Improved natural grassland (ING) and NG presented a higher density and root diameter than PP and annual pasture (AP). Forage systems significantly influenced soil porosity and density, with NG and ING showing lower soil densities and higher soil porosities. The OCS (0–100 cm) was similar between NG (270 Mg ha–1), ING (255 Mg ha–1), PP (274 Mg ha–1), and AP systems (256 Mg ha–1). Over a period of five years, the intensification of pasture-based animal production systems did not have a significant impact on OCS in the soils of a Brazilian subtropical highland.