Threats to sustainable food production are accelerating due to climate change, depletion of natural capital, and global financial instability. This causes significant risks to farmers, consumers, and financial and policy institutions. To better understand and forecast alternative futures for agricultural production, we have developed a dynamic simulation model that accounts for the core natural capital components of agro-ecosystems, including climate, soil, carbon, water, nitrogen, phosphorus, microorganisms, erosion, crops, grazing, and trees. Understanding agro-ecosystems, and how varying management styles impact long-term local and global risks, is critical to future wellbeing. The model can be used to simulate dynamics of soil health and project it into the future to assess vulnerabilities and resilience. This knowledge can inform and guide investment decisions by financial institutions, insurance companies, farmers, and government agencies. Here, we describe the basic model structure, sensitivity, and calibration results. We then run a few scenarios to highlight the model’s ability to analyze the results of alternative agro-ecosystem management options.