Carotenoids have attracted significant interest due to their potential use in human health and nutrition, and their global demand increases by 3.7% annually. Currently, synthetic carotenoids dominate the market, but possess challenges such as low antioxidant ability, issues with health benefits, and safety concerns. Microalgae are potential producers of natural carotenoids with extraordinary antioxidant properties, although the yield is often low in their natural cycle. The present investigation aimed to analyze the effect of multiple abiotic factors on enhancing algal carotenoids synthesis and other metabolites without affecting growth. The potential microalgae Monoraphidium sp. were grown under altered nutrient and light conditions employing RSM-CCD. The optimized conditions, such as Nitrogen (5 g·L−1), Phosphorus +Potassium (250 mg·L−1), Sulphur (70 mg·L−1), and light (137.5 µmol·m−2·S−1), resulted in increased biomass (1357.36 mg·L−1), lipid accumulation (40.28% of dry biomass), and carotenoids (16.26 µg·mL−1) as compared to the control conditions. The total carotenoids fraction consisted of astaxanthin (14.8%), violaxanthin (3.61%), lutein, (45.12%), 9-cis-β carotene (7.62%), and β-carotene-5,6-epoxide (24.21%). Among them, violaxanthin (1.32-fold), astaxanthin (1.19-fold), 9-cis- β carotene (1.07-fold), and β-carotene-5,6-epoxide (1.08-fold) content increased while lutein (1.32-fold) content decreased significantly. The improvement in algal carotenoids under novel culture conditions provides a significant advantage to pharmaceutical and nutraceutical industries.