The biomass ensilage conversion (BEC) system is an integrated process for production of organic acids, mainly lactic and acetic acid, and pretreatment and storage of high lignocellulosic materials. Iodoform has been found to selectivity inhibit certain microbes and may help to inhibit undesirable silage microbes. Manure presents a source of nutrients for amending biomass. The objectives of this thesis were to examine the effect of iodoform and manure on fermentation in the BEC system for corn stover. 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 and ensiled for 21 days. 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. 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 and presumably clostridia activity when applied at a rate of 0.23 g/kg DM. Corn stover-manure mixtures were prepared containing manure at rates of 0, 15, 30, 45, and 60 % while and ensiled for 21 days. 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, with the 30, 45, and 60 % manure rates producing the highest concentration of 1.8 % DM. These results indicate that iodoform can improve fermentation in this hybrid ensilage system by increasing lactic acid production and inhibiting butyric fermentation. Treatments of 0, 15, 30, and 45% manure would be acceptable substrates for use in this system, however if pretreatment is a higher priority than organic acid production the pure corn stover substrate would be the most appropriate material to use.