Wastewater utilization by microalgal strains is due to changes in the inherent phenotypic traits that enable metabolic flexibility, facilitating their adaptation to survive in harsh environments. However, the potential role of changed phenotypic traits such as physiological and metabolic activities required for enhanced biomass production remains largely underexplored. In this study, involving acid-tolerant microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, we observed a timedependent growth increase (>300% after 1 week) under mixotrophic conditions. While transitioning to the second week, there was a change in growth pattern, with >600% increase in chlorophyll content and minor pH alterations, indicating the phenotypic response to the synergistic effect of nutritional mode during wastewater treatment. Both the strains showed a similar removal (70−80%) of both organic and inorganic carbon present in the wastewater, while the removal of nitrogen and phosphate (80−90%) was significant during mixotrophy. Metabolic analysis revealed the prominence of key pathways such as CO 2 fixation, nitrogen assimilation, and amino acid metabolism under mixotrophic conditions of an open system. Especially, strain MAS1 exhibited elevated expression of organic acids, suggesting their crucial role in nutrient uptake from winery effluents during mixotrophy. Thus, our study demonstrates that a synergy of wastewater environment and nutritional mode enhances phenotypic trait expression in microalgae to improve metabolic flexibility and sustainable biomass production.