The aim of the research is to identify the changes which occur in lignin from miscanthus and sorghum, one of the main biomass components, as a result of an anaerobic digestion (AD) process. The percentage content and structure of lignin before and after the fermentation process were analysed using biomass harvested in two growing periods—before and after vegetation. It was shown that plants at different developmental stages differ in lignin content. During plant growth, the lignin structure also changes—the syringyl-to-guaiacyl ratio (S/G) increases, whereas the aliphatic and aromatic structure ratio (Al/Ar) decreases. The AD process leads to an increase in percentage lignin content in cell walls, and the increase is higher for plants harvested during vegetation. It has been shown in studies that the methane fermentation of miscanthus and sorghum produces waste containing a large amount of lignin, the structure of which is altered relative to native lignin. The quantity and the new, simplified structure of lignin create new possibilities for using this aromatic polymer.