The conservation of natural ecosystems is an essential component for sustainable land use (LU). One of the challenges facing society worldwide is climate change, where reduce emissions, and sequestrate greenhouse gases from the atmosphere are fundamental to mitigate its effects. LU change plays a major role in the carbon (C) cycle, and understanding and quantifying its effects is one of the main challenges for effectively implementing climate change mitigation actions. Given this scenario, our objective was to calibrate the Daycent model to estimate the references equilibrium soil organic matter (SOM) for three important Brazilian biomes: Atlantic Forest (AF), Cerrado (CE), and Pampa (PA). Together, they represent 39% of native vegetation area, and over them are concentrated the majority of the agricultural production in Brazil. Estimating the equilibrium for major soil types in the three biomes is fundamental for evaluating C dynamics and the soil C loss regarding LU changes. Data from literature, including SOM, were collected for the three biomes: PA (29°30’S, 54°15’W; soil with sandy loam texture), CE (19°28’S, 44°15’W; very clayey texture) and AF (10°92’S, 37°19’W; sandy texture). Daycent parameters to represent the biomes biophysical properties were initially set up with values from local literature. Measured SOM was then employed during the calibration of the Daycent model. We ran the model for 6,000 years for the equilibrium simulations, obtaining the stabilization of the SOM compartments (active, slow, and passive). For the biomes’ biophysical properties the parameters for maximum potential production (PRDX) were adjusted for each biome, PA with 0.92 g C m-2 , AF with 1.5 g C m-2 and CE with 0.9 g C m-2 (default = 0.5 g C m-2). The relative error between measured and predicted total SOM was lower than 2% for all biomes, thus representing the equilibrium properly for the study conditions. The largest C compartment of the biomes (slow organic matter in the soil) had 71.7% for AF, 68.5% for PA, and 63.7% for CE of the total SOM. The highest SOM values were found in the CE, with 53 Mg C ha-1, followed by the PA with 37 Mg C ha-1, and in the AF with 35 Mg C ha-1. Eventual LU changes will impact the SOM equilibrium of these native vegetation, but sustainable practices must take place to avoid C losses as far as possible.