<p>Owing to the soaring demand of sustainable nutraceuticals, cosmetics and pharmaceuticals, the yeast-based carotenoid synthesis has attracted a lot of attention. Yeasts have the inherent capacity to synthesize an array of carotenoids including β-carotene, astaxanthin, lycopene, and zeaxanthin. Exploitation of yeasts for carotenoid production offers a natural and cost-effective solution to meet the growing demand of natural carotenoids. Although wild-type strains naturally synthesize carotenoids, however the low yields, limited metabolic pathways, competition with endogenous pathways, and sensitivity to environmental factors lead to suboptimal production efficiency. Development of engineered strains with high yields and resilience to abiotic and biotic stressors is thus required for commercialization. In this regard, metabolomics analysis of the target yeast cultivated in different conditions can lead to identification of key targets that could be exploited for enhancing the carotenoid synthesis via gene editing. Within the field of metabolomics, techniques like advanced metabolite quantification and flux balance analysis provide in-depth understanding on the yeast’s metabolism and carotenoid biosynthesis. Notably, the use of CRISPR-Cas9 for precise gene editing for reshaping the genotype for maximizing carotenoid productivity is gaining momentum. The methodologies of synthetic biology and the principle of directed evolution additionally enhance the function of enzymes, ligand-binding and regulatory elements, which in turn sustains the equilibrium of the synthesizing pathway at the high level of expression. The present review provides a comprehensive analysis of the carotenoid production using genetic engineered strains. Moreover, the review underscores the transformative potential of metabolomics approaches for identifying novel genetic engineering targets in yeasts. The cost-competitiveness of yeast-based carotenoids along with challenges and future perspectives is also discussed.</p>