Pathway analysis of metabolomic and proteomic data is critical for understanding the intricacies of biological processes and disease mechanisms. The challenging process of pathway analysis has become less burdensome thanks to online tools and databases that enable the comparison of pathways in intricate biological systems. Data analysis tools, like MetaboAnalyst 6.0, evaluate complex interactions and metabolic networks in biological pathways. Metabolomic and proteomic data integration is performed by utilizing databases, like KEGG, to analyze pathways and determine the interplay of proteins, metabolites, and other molecules in common pathways. Molecular interactions and similarities between pathways are explored to promote hypothesis generation and guide further research. This comprehensive chapter will enhance the understanding of utilizing pathway analysis of metabolic and proteomic data of various conditions, biomarkers, organisms, and therapeutic molecular targets, paving the way for future investigations and clinical applications, especially in pharmacology. Drugs like Metformin can be studied more extensively with pathway analysis, as demonstrated in this chapter, to enhance our understanding of how drugs affect patients.