Lutein available in the current market is derived from marigold petals. However, extensive studies showed that microalgae are rich in lutein content and potentially exploitable for its dietary and other industrial applications. In this study, microwave assisted binary phase solvent extraction method (MABS) was the novel protocol being developed and optimized to achieve maximum lutein recovery from microalgae Scenedesmus sp. biomass. Results showed that 60% potassium hydroxide solution with acetone in the ratio of 0.1 (ml/ml) was the ideal binary phase solvent composition. Empirical model developed using response surface methodology revealed highest lutein content can be recovered through MABS extraction method at 55 °C treatment temperature, 36 min in extraction time, 0.7 (mg/ml) for biomass to solvent ratio, 250 Watt microwave power and 250 rpm stirring speed. This optimized novel protocol had increased the amount of lutein recovered by 130% and shorten the overall extraction time by 3-folds.