Ensilage is increasingly viewed as a low-cost, low-risk alternative to traditional dry storage methods for biomass, especially in humid regions of the US. During the long months of storage, it may be possible to enhance the value of biomass by incorporating a biological pretreatment strategy to partially break down lignin. In this study white rot fungi were inoculated into corn stover biomass and grown in an aerobic cycle to investigate whether they could effectively degrade the lignin fraction of corn stover. Three different fungi, Phanerochaete chrysosporium, Ceriporiopsis subvermispora, and Fusarium proliferatum were tested for their abilities to degrade lignin efficiently under these conditions. The aerobic cycle was implemeneted either before or after a 7 day ensilage process, for periods of 7 and 14 days. Fungal pretreatment does appear capable of significant degradation of the lignin fraction. However, results also indicated important tradeoffs between lignin degradation and dry matter loss. Pretreatment effects on subsequent fermentation was also investigated. Optimization of this process may help reduce these negative impacts and create an economically viable biological pretreatment strategy.