This study evaluated Carbon (C) storage in different compartments in eucalyptus stands and native Cerrado vegetation. To determine C above ground, an inventory was carried out in the areas where diameter at breast height (DBH), diameter at base height (Db), and total tree height (H) were measured. In the stands, the rigorous cubage was made by the direct method, and in the native vegetation, it was determined by the indirect method through an allometric equation. Roots were collected by direct method using circular monoliths to a depth of 60 cm and determined by the volume of the cylinder. Samples were collected up to 100 cm deep to estimate C stock in the soil. All samples collected directly had C determined using the CHNS elemental analyzer. Gas samples were collected using a manually closed chamber, and the gas concentration was determined by gas chromatography. The results indicate high C storage in the studied areas > 183.99 Mg ha−1, could contribute to CO2 mitigation > 674.17 Mg ha−1. In addition to low emissions (<1 kg ha−1 yr−1) for the three evaluated areas, with no statistical difference in relation to the Global Warming Potential. Concerning the native cerrado vegetation conversion, the “4-year-old eucalyptus stand” seemed to restore the original soil carbon stocks in the first-meter depth, regardless of some losses that might have occurred right after establishment. Conversely, a significant loss of carbon in the soil was observed due to the alternative setting, where similar natural land was converted into agriculture, mostly soybean, and then, years later, turned into the “6-year-old eucalyptus stand” (28.43 Mg ha−1). Under this study, these mixed series of C baselines in landscape transitions have reflected on unlike C dynamics outcomes, whereas at the bottom line, total C stocks were higher in the younger forest (4-year-old stand). Therefore, our finding indicates that we should be thoughtful regarding upscaling carbon emissions and sequestration from small-scale measurements to regional scales