Ag_EcoSOpt is an open-source software-based decision-support tool that incorporates the concepts of ecosystem modelling, ecosystem services tradeoffs, economic valuation and optimization, and land management and land use change decision making in agricultural production systems. It has two main components with several attached modules. The ecological qualification component is used to quantify changes in ecosystem functions (e.g. greenhouse gas emissions, soil organic matter, water loss, nitrogen leaching, crop yield, and crop residue) in response to changes in human decision making on land management practices or land uses. It integrates two core models: (1) DAYCENT, a biogeochemical model created by the Natural Resources and Ecology Laboratory at Colorado State University; and (2) The Greenhouse Gases, Regulated Emissions, and Energy Use in Transportation Model (GREET) created by Argonne National Laboratory. The optimization component includes a spreadsheet-based module or standalone MATLAB application for farm-gate optimization or supply chain optimization of end use products (e.g. grain for cattle feed or biofuel, biomass for electricity or biofuel). Ag_EcoSOpt supports multilevel decision making for crop lands in the United States such as individual farms or landscape, user-defined time frames (1-50 years), and farm-gate or supply chain analysis.