Sustainable aviation fuels (SAF) produced from lipid feedstocks are an increasingly mature and low-cost option for aviation sector decarbonization. Ethiopian mustard (Brassica carinata) is a non-food oilseed crop that can be grown on winter fallow land in the southeastern US and used as a feedstock for SAF, with a high-protein livestock feed co-product. Integrating carinata into existing annual crop rotations produces an additional revenue stream for landowners, with potential co-benefits for soil carbon and other ecosystem services. The Southeast Partnership for Advanced Renewables from Carinata (SPARC) is a USDA-funded research consortium to advance carinata production and associated SAF and bioproduct supply chains in the region. A SPARC research team used the DayCent ecosystem model to estimate the potential production of carinata across the tri-state region of Alabama, Florida, and Georgia, and assess associated changes in soil carbon storage and emissions of nitrous oxide (N₂O), the main biogenic greenhouse gas (GHG) emissions from agriculture. First, we calibrated DayCent to reproduce the phenology, harvest index, productivity response to nitrogen application, root-to-shoot biomass ratio, and tissue nitrogen content data observed for a set of carinata field trials in the region. Next, we simulated the integration of carinata into a typical cotton/peanut rotation across the 2.3 million hectares of annual cropland within the climate suitability range for this crop, grown once every third winter. We show an annual production potential of greater than 1 billion liters of SAF from this feedstock in the region. Our base carinata management case is approximately neutral in biogenic GHG emissions, with modest soil carbon sequestration that offsets the associated small increase in N₂O emissions. However, adopting conservation management practices such as no-till establishment or poultry litter soil amendments results in a more substantial net soil carbon sink, reducing the GHG footprint of carinata-derived SAF by up to 20 grams of CO₂-equivalent per megajoule of fuel. This work supports SPARC’s ongoing efforts to develop improved crop varieties and management practices that simultaneously improve the economics and ecosystem service value of carinata production.