The Cerrado biome covers approximately 20% of Brazil and it is crucial for the Water, Food, Energy, and Ecosystems (WFEE) nexus. Thus, in recent years, large areas of the undisturbed Cerrado have been converted into farmland. In this biome, according to the Brazilian Forest Code, farmers need to keep 20% of native vegetation (Legal Reserves - LRs). By exploring combined and isolated impacts of different scenarios of LR and Protected area (PA) arrangements, this study evaluated the importance of complementarity between LR compliance and the amount of PAs (including Conservation Units - CUs and Indigenous Lands - ILs) to reduce deforestation and conserve native vegetation in the Cerrado. Seven scenarios were investigated: a scenario that considers the current PA and the LR values foreseen in the Native Vegetation Protection Law - NVPL; three scenarios focused on production; and three focused on conservation. Considering the trend of the current scenario, the estimated loss of native vegetation will be 30% (30.6 million ha) by 2070. According to the model simulations, for two periods (2050 and 2070), the LR Elimination scenario (LRE) would cause a greater loss of native vegetation than the PA Elimination (PAE), and as expected, the exclusion of both (PALRE) would provide a greater loss of native vegetation. Native vegetation is concentrated mainly on agricultural properties. Taking our conservation-oriented scenarios as an example of conservation strategies, if there were no financial, practical, political, social or personal constraints, there is no doubt that the CPALRI scenario (Creation of Protected Areas and Legal Reserve Increase) is the best trajectory for conserving biodiversity. Therefore, private properties, through LRs, are essential for efficient planning of land use/cover as they ensure security in the WFEE nexus. The resulting projected scenarios are important to help decision makers in territorial planning and how to arbitrate territorial demands aiming at the rational use of the natural resources of the Cerrado.