Shikimic acid (SA) is a critical starting material for production of the anti-influenza drug oseltamivir phosphate. In this study, microbial productions of SA from corn grain and corn stover are compared using life cycle assessment (LCA) and technoeconomic analysis (TEA). The life cycle impacts considered in the study include global warming potential, eutrophication potential, water usage, and land usage. Results of LCA depended on assumptions of allocation. As a waste product, stover contributed 15% more than grain to global warming, 86% less to eutrophication, 96% less to water usage, and 69% less to land usage. With allocation based on the economic value of the feedstocks, stover contributed 33% more than grain to global warming and had eutrophication, water usage, and land usage impacts that were over 2-fold higher than those of corn grain. TEA indicated that both biorefinery models were profitable. SA sourced from corn grain is more profitable than SA sourced from corn stover. This work quantifies improvements needed to make the market for stover-derived glucose and xylose mixtures more competitive than that for grain-derived glucose. Minimizing the economic gap between these processes requires higher sugar yields from milled corn stover and improved SA yields from stover-derived sugar feeds.