Corn bioethanol production generates large volumes of animal feed coproducts with nutritional value largely determined by their fiber and protein content. Here, we combined microscopic and biochemical lignin quantification, and proteomic analysis to characterize the corn flour (CF) feedstock and downstream dried distiller’s grains with solubles (DDGS) and corn fermented protein (CFP) fractions from an industrial bioethanol plant. We show that the industrial processing concentrates lignin up to 8% of the dry weight of distiller grain fractions, representing an opportunity for its recovery and utilization. We also characterized the proteome of these materials, identifying ~4,200 maize (Zea mays) proteins, and ~300 yeast (Saccharomyces cerevisiae) and ~90 bacterial (Escherichia coli) proteins. Interestingly, 90% of the maize proteins present in the CF feedstock were detected in the DDGS and CFP fractions, suggesting mild protein breakdown during processing. Proteomics analysis enabled us to map the abundance levels of specific enzymes involved in lignin and starch biosynthesis in the maize endosperm, and key yeast enzymes involved in the glycolysis and fermentation pathways, revealing limiting enzymatic steps in these metabolic pathways. Additionally, we found that seed storage proteins, particularly globulins and oleosins, were enriched in the high-protein CFP fraction, consistent with its higher nutritional value. Microbial proteomics revealed that S. cerevisiae and E. coli each contributed ~3% of the total protein present in DDGS and CFP fractions. This study provides the first proteomic analysis of corn ethanol coproducts and identifies targets to enhance their utilization via maize genetics, microbial engineering, or lignin valorization strategies.