Plants produce a vast array of bioactive secondary metabolites, including phenylpropanoids, terpenoids and alkaloids that are essential for ecological adaptation and serve as critical resources for the pharmaceutical, cosmetic, and agrochemical industries. However, the low natural abundance of these compounds and the over-harvesting of medicinal species have created a significant supply-demand gap. This article provides a comprehensive overview of traditional and emerging strategies for the elucidation of plant biosynthetic pathways, a prerequisite for enhancing yields through genetic engineering and synthetic biology. Foundational biochemistry-based approaches was examined, such as stable isotope labelling and enzyme kinetics, and contrast them with modern "omics" technologies. The integration of genomics, transcriptomics, proteomics and metabolomics collectively termed "herbgenomics" has revolutionized the field by enabling the identification of biosynthetic gene clusters (BGCs), tissue-specific expression patterns and active protein landscapes. Furthermore, the review explores the role of computational tools, machine learning and synthetic biology in reconstructing complex metabolic networks in heterologous hosts like yeast and bacteria. Finally, the transformative potential of CRISPR/Cas9 genome editing was discussed for functional gene validation and metabolic flux optimization. By synthesizing these multi-disciplinary approaches, this article outlines a holistic roadmap for deciphering specialized metabolism and ensuring the sustainable production of high-value phytoconstituents.