Lignin, a complex plant polymer, represents an abundant but underutilized biomass resource, with its breakdown products offering potential for sustainable bioprocessing. Using a multi-omics approach, comparative genomics, proteomics, and metabolomics, we identified a novel oxidative pathway for pinoresinol, a model lignin dimer for β-β′ linkage, degradation in Pseudomonas sp. strain SG-MS2. The pathway is initiated by a flavoprotein from the VAO/PCMH enzyme family, requiring a cytochrome partner for activity, which we functionally validated as the first gene in this catabolic route. This discovery not only elucidates a unique mechanism for microbial lignin-derived dimer degradation but also highlights its potential for industrial applications, such as the biosynthesis of vanillin and other valuable chemicals. Our findings demonstrate the power of omics-driven approaches in uncovering novel metabolic pathways and advancing lignin valorization strategies.