This study investigated the fate of lignocellulosic biomass (wheat-feed and perennial rye grass) in different anaerobic digestion systems, evaluating the role of substrate specificity on the pattern of degradation. The two-stage (biohydrogen-biomethane) anaerobic system was found to be more effective in the degradation of lignocellulose, when compared to the conventional single-stage system. The perennial rye grass substrate possessed about 21% higher holocellulose concentration when compared to the wheat-feed; its exploitation in the acidogenic digestion was however poor, resulting in a 2.9% lower biogas yield in a equivalent two-stage system. The study therefore developed a treatment technique involving the use of cellulase and ferulic acid esterase enzyme combinations for the treatment of perennial rye grass. The enzyme cocktail at 0.202 ml enzyme/g VS added resulted in efficient bioconversion of the complex polymers to soluble carbohydrates, evident in the yield increase of soluble COD, to 321.0±10.9 mg/gVS, a 393.2% yield increase, when compared to the no enzyme added control. The yield of bio-hydrogen after enzymatic addition was 48ml/gVS, 335% higher when compared to the alkaline treatment; and more than seven fold higher than the yield obtained from the fermentation with no pre-treatment. The acetate to butyrate ratio varied from 4:1, when no pre-treatment was used, to 2:1when alkaline pre-treatment was used, then to 1:1 after the enzymatic treatment. The downstream effect of the prior hydrolysis on the subsequent processes to acidogenic fermentation like biomethane and PHA production and lignin recovery were also investigated. The hydrogenic/acidogenic fermentation resulted in methane yield improvement of 45.7%. The study shows that the more effective a hydrolysis procedure is in the depolymerisation of complex polymers, the greater the accumulation of PHA in the PHA biosynthesis operations. The enhanced hydrogenic /acidogenic fermentation having effectively degraded the holocellulose component of the perennial rye grass substrate ensured that relatively high quality lignin was obtained in an Organosolv lignin-extraction procedure. FT-IR profile show less contamination of polysaccharides and proteins in the lignin extracted from the enzymatically enhanced acidogenic fermentation. An evaluation of the economic viability of the investigated secondary processes showed that direct integrations of those processes to the biohydrogen process may not be as economically advantageous, when compared to a 2nd -stage biomethanation system.