The diverse perspectives offered by multi-omics data analysis can aid in identifying the most relevant molecular pathways involved in disease processes, and findings in one layer can substantiate findings in other layers of information. Integrating data from multiple omics sources is becoming increasingly important to improve disease diagnosis and treatment, especially for conditions with complex and poorly understood underlying pathomechanisms. Methylmalonic aciduria (MMA), an inherited metabolic disorder, serves as an illustrative example of such a disease with poorly understood pathogenesis for which published multi-omics data are readily available. Re-using these FAIR data, obtained from the multi-omics digitization of 230 MMA patient samples, we pursued advanced data integration and analysis strategies to integrate different levels of biological information, combining genomic, transcriptomic, proteomic, and metabolomic profiling with biochemical and clinical data, with the aim of elucidating molecular perturbations in individuals affected by MMA. The analysis of protein-quantitative trait loci highlighted the importance of glutathione metabolism in the pathogenesis of methylmalonic acidemia (MMA). This finding was supported by correlation network analyses that integrated proteomics and metabolomics data, alongside gene set enrichment and transcription factor analyses based on disease severity from transcriptomic data. The correlation network analysis also revealed that lysosomal function is compromised in MMA patients, which is critical for maintaining metabolic balance. Our research introduces a comprehensive data analysis framework that effectively addresses the challenge of prioritizing disruptions in molecular pathways by accumulating evidence from multiple omics levels.