Thermal hydrolysis process (THP) and biological hydrolysis (BH) are key pre-treatment technologies for anaerobic digestion (AD), termed advanced anaerobic digesters (AADs). They target the rate-limiting hydrolysis step in AD. This study evaluates full-scale pre-treatments for macromolecule bias and the implementation of hydrolysis enzymes to enhance biogas yield. Findings show THP significantly improves protein and carbohydrate solubilisation by 30% and 25%, respectively, but fully hydrolyses only carbohydrates. In contrast, BH targets fibres and proteins, achieving 35% and 23% solubilisation, and only partially hydrolyses carbohydrates. Biomethane potential (BMP) tests indicate that protease enzymes raise biomethane yield by 20-30% for AAD with THP pre-treatment. In comparison, α-amylase increases it by over 30% for AAD with BH pre-treatment. This study tailors enzyme selection and dosage to specifically address the unique "hydrolysis blind spot" of each pre-treatment, providing a strategic framework to enhance AD technologies by an improved understanding of macromolecule selectivity and their transformation pathways.