Agricultural lands occupy 38% of global land surface and are expected to grow significantly in the next years, increasing the need for more sustainable practices, as well as better informed conservation practices of natural ecosystems. Carbon stocks are important estimates for the assessment of potential emissions caused by deforestation, and therefore widely used in strategies to mitigate climate change in agroforestry systems. Although research on biomass and carbon accumulation in agricultural lands is well documented, comparisons with adjacent natural forest areas are uncommon, mainly in tropical regions. Here, we used forest inventory data and allometric models to estimate biomass and carbon stocks of natural vegetation types (gallery forest-GF, morichal-MOR, and savanna-SAV) and oil palm (Elaeis guineensis) crops in the Orinoquía bioregion, in Eastern Colombia. We found that natural forests (GF and MOR) hold 542.45 Mg ha−1 of aboveground biomass, whereas oil palm plantations store 284.87 Mg ha−1. Morichal vegetation, commonly known as peat swamp forests, accumulated the highest aboveground biomass and carbon per hectare among all vegetation types (natural and agricultural), with an estimate of 402.76 Mg ha−1. Thus, although oil palm crops are great reservoirs of biomass and carbon at the landscape level, it is the combination of natural and agricultural lands which assure highest carbon sequestration in the study area. These results highlight the importance of preserving natural areas in agricultural landscapes for climate mitigation and conservation of biodiversity, which may jointly benefit plantations sustainable development.