Applying material balance calculations to the evaluation and optimization of lignocellulosic biomass conversion processes is fundamentally important. The lack of a general framework for material balance calculations and inconsistent compositional analysis data have made it difficult to compare results from different research groups. Material balance templates have been developed to follow accurately the distribution of carbon in lignocellulosic substrates through the pretreatment and simultaneous saccharification and fermentation (SSF) processes, and provide information on overall carbon recovery, recovery of individual sugars, and solubilization of biomass components. Based on material balance considerations, we developed equations that allow us to compute overall ethanol yields for biochemical conversion of biomass correctly.