The technologies currently in place to convert lignocellulosic biomass to energy are either biochemical or thermochemical, the efficiencies of which may vary depending on the composition of the feedstock. One variable that conversion technologists have wrestled with, particularly in the simultaneous saccharification and fermentation process, is biomass lignin content. While lignin is considered a recalcitrant to biochemical conversion, it can be a good source of combustion fuel, but the true effect of composition on thermochemical conversion has not been well quantified. In this study we examined the effect of lignin content of alfalfa stems on two biofuel conversion methodologies: (i) biochemical conversion using in-vitro ruminal fermentation as a surrogate for fermentability to ethanol and (ii) thermochemical conversion using pyrolysis. Lignin was found to account for little of the variation in pyrolysis product yield compared to biochemical conversion. Linear regression of lignin concentration on pyrolysis product yields resulted in few significant relationships whereas in-vitro gas production exhibited a strong negative response to lignin content. For alfalfa stems, lignin had a much larger effect on biological conversion potential than it did on thermochemical conversion potential. The results suggest that genetic modification or agronomic management of lignocellulosic biomass for bioenergy feedstock composition should be based on the intended energy conversion platform.