Iodoform, an iodine-containing compound used in antiseptic applications, has been found to be effective at selectivity inhibiting certain microbial populations. Application of iodoform in a hybrid fermentation system was investigated to determine the potential for increased lactic acid production by inhibiting undesirable microbes which can metabolize lactic acid. Iodoform treatment rates of 0, 0.03, 0.06, 0.11, and 0.23 g/kg dry matter (DM) were applied to a swine manure-corn stover substrate, containing 60 % manure, adjusted to 65 % moisture on a wet basis and ensiled for 0, 1, 7, and 21 days. A hemicellulase-cellulase enzyme mixture was also applied to all samples at a rate of 5 and 12.5 IU/g DM of hemicellulase and cellulase activity, respectively. Samples were analyzed for pH, water soluble carbohydrates, and organic acids. A substantial decrease in pH was observed in all treatments, but none of the treatments reached a pH of 4.5, which is sufficient for stable storage of corn stover biomass at 65 % moisture. Lactic and acetic acid production was increased with application of iodoform at 0.23 g/kg DM. Iodoform was also found to inhibit butyric fermentation, with a rate of 0.23 g/kg DM determined to be appropriate. Overall, iodoform can improve fermentation in the biomass ensilage conversion system by improving lactic acid production and inhibiting butyric fermentation.