Pretreatment of lignocellulosic biomass is both chemically and economically intensive. Improving the quality of biomass during storage can reduce the severity of pretreatment and benefit other downstream processes. Ensilage is anaerobic solid state fermentation, where the production of organic acids creates an acidic environment, typically pH 4.0. The severe conditions inhibit microbial growth and preserve biomass. Trichoderma reesei Rut C30 is a filamentous fungus that produces cellulases and xylanases when grown aerobically on lignocellulosic biomass at 30 C. The fungus converts polysaccharides to sugars but also consumes a considerable amount of biomass for its growth. Performing ensilage after obtaining some polysaccharide conversion may control both polysaccharide conversion and biomass loss. Two different experiments with 7 and 14 days of aerobic phase were conducted. The effect of sterilization of biomass prior to fungal growth was studied with 7 days of aerobic phase. The effect of a higher temperature (50 C) on enzyme activity and polysaccharide conversion was studied with 14 days of aerobic phase. In both the experiments, ensilage was performed before and after fungal growth separately to determine the optimal order of anaerobic and aerobic phases. The processes with aerobic phase after ensilage consumed the organic acids produced increasing the pH levels back to 6.0. Higher temperature caused higher dry matter (DM) loss of about 0.4 g/g initial DM compared to 0.15 g/g initial DM. Surprisingly, sterilized biomass exhibited higher loss of dry matter. The best process was considered to be 7 days of aerobic phase before ensilage on unsterile stover, which produced similar polysaccharide conversion to 14 days of aerobic phase but significantly lower dry matter loss.