Threats to sustainable food production are accelerating due to climate change, population growth, depletion of natural capital, and global market instability. This causes significant risks to farmers, consumers, and financial and policy institutions. Understanding agro-ecosystems, and how varying management styles can impact their performance is critical to future wellbeing. To better understand and manage 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, farm animals and plants. Dynamic Agro-Ecosystem Simulation (DAESim) 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 governmental agencies. Here, we describe the basic model structure, sensitivity, and calibration results. We then run a few scenarios to demonstrate the model's ability to analyze alternative agro-ecosystem management options.