With the development of agricultural biorefineries and bioprocessing operations, understanding the economic efficiencies and environmental impacts for these have gradually become popular for the deployment of these industrial processes. The corn-based ethanol and soybean oil refining industries have been examined extensively over the years, especially details of processing technologies, including materials, reaction controls, equipment, and industrial applications. The study focused on examining the production efficiency changes and economic impacts of integrating products from the enzyme-assisted aqueous extraction processing (EAEP) of soybeans into corn-based ethanol fermentation processing. Using SuperPro Designer to simulate production of corn-based ethanol at either 40 million gallons per year (MGY) or 120 MGY, with either oil separation or no oil removal, we found that indeed integrating soy products into corn ethanol fermentation may be slightly more expensive in terms of production costs, but economic returns justify this integration due to substantially greater quantities of ethanol, distillers corn oil, and distillers dried grains with solubles being produced.