In this research, we investigated the impact of drought stress on secondary metabolite production in cumin plants and the associated transcriptional changes in biosynthetic genes. Drought stress induced a significant increase in the levels of beta-carotene, lycopene, terpenes, anthocyanin, phenolic compounds, flavonoids, and alkaloids, indicating an adaptive metabolic shift in response to adverse conditions. Concurrently, there was an upregulation in the expression of key biosynthetic genes, including Phenylalanine ammonia-lyase (PAL), 3-deoxy-7-phospho-heptulonate synthase (DAHP synthase), Deoxy xylose phosphate reductase (DXS), 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), and Geranyl diphosphate synthase (GPPS), which corroborated the metabolite findings. Notably, while most secondary metabolites exhibited an increasing trend under drought stress, flavonoids dis-played a disproportionate elevation, even as there was an overall decrease in phenolic compounds and other metabolites. This observation suggests the potential activation of alternative flavonoid synthesis pathways or the conversion of phenolic compounds to flavonoids during stress. Strong correlations were identified between the expression of biosynthetic genes and their respective metabolite concentrations, underscoring the central role of transcriptional regulation in secondary metabolite synthesis during drought stress. Collectively, our results provide a comprehensive understanding of the transcriptional and metabolic adaptations of cumin plants when exposed to drought stress. Such insights can be pivotal in designing drought-resilient crops, with significant implications for food security amidst escalating climatic challenges.