Swine manure contains a host of chemical and biological constituents which make it desirable for amending lignocellulosic biomass in storage for year round processing in a biorefinery. Application of swine manure in an integrated biomass storage and conversion system was investigated to determine the potential for improved conversion of corn stover to organic acids and soluble carbohydrates during ensiling. Corn stover- swine manure mixtures were prepared containing swine manure at rates of 0%, 15%, 30%, 45%, and 60% while simultaneously being adjusted to 65% moisture on a wet basis and ensiled for 0, 1, 7, and 21 days. Samples were analyzed for pH, dry matter, water-soluble carbohydrates, and organic acids. All treatments, with the exception of the 60% manure substrate, produced a pH less than 4.5, which is sufficient for stable storage. Water-soluble carbohydrates were highest in the control treatment, producing a level of 3.0% DM at day 21. Lactic acid production was unaffected by the rate of manure, with a concentration of 2.8% DM reached at day 21. Acetic acid production was improved with the manure substrates. Manure amendment rates of 30%, 45%, and 60% produced the highest acetic acid concentration of 1.8% DM. Treatments of 0%, 15%, 30%, and 45% swine manure would be acceptable substrates for use in this system; however, if preservation of fermentable carbohydrates is a higher priority than organic acid production, then the pure corn stover substrate would be the most appropriate material to use.