Lignocellulosic biomass represents the only renewable carbon resource which is available in sufficient amounts to be considered as an alternative for our fossil-based carbon economy. However, an efficient biochemical conversion of lignocellulosic feedstocks is hindered by the natural recalcitrance of the biomass as a result of a dense network of cellulose, hemicelluloses, and lignin. These polymeric interconnections make a pretreatment of the biomass necessary in order to enhance the susceptibility of the polysaccharides. Here, we report on a detailed analysis of the favourable influence of genetic engineering for two common delignification protocols for lignocellulosic biomass, namely acidic bleaching and soda pulping, on the example of CAD deficient poplar. The altered lignin structure of the transgenic poplar results in a significantly accelerated and more complete lignin removal at lower temperatures and shorter reaction times compared to wildtype poplar. To monitor the induced chemical and structural alterations at the tissue level, confocal Raman spectroscopy imaging, FT-IR spectroscopy, and X-ray diffraction were used.