Development of biomass feedstocks with desirable traits for cost-effective conversion is one of the main focus areas in biofuels research. As suggested by techno-economic analyses, the success of a lignocellulose-based biorefinery largely relies on the utilization of lignin to generate value-added products, i.e. fuels and chemicals. The fate of lignin and its structural/compositional changes during pretreatment have received increasing attention; however, the effect of genetic modification on the fractionation, depolymerization and catalytic upgrading of lignin from genetically engineered plants is not well understood. This study aims to fractionate and characterize the lignin streams from a wild-type and two genetically engineered switchgrass (Panicum virgatum) species (low lignin content with high S/G ratio and high lignin content) using three different pretreatment methods, i.e. dilute sulfuric acid, ammonia hydroxide, and aqueous ionic liquid (cholinium lysinate). The structural and compositional features and impact of lignin modification on lignin-carbohydrate complex characteristics and the deconstruction of cell-wall compounds were investigated. Moreover, a potential way to upgrade low molecular weight lignin to lipids by Rhodococcus opacus was evaluated. Results from this study provide a better understanding of how lignin engineering of switchgrass influences lignin fractionation and upgrading during conversion processes based on different pretreatment technologies.