In this study, a biorefinery process integrating dark fermentation with microalgae cultivation (dual phase metabolic transition) was demonstrated with real-field wastewater. Acid rich fermented effluents (distillery waste (FDW1); dairy waste (FDW2)) were used as feedstock for microalgae cultivation. Experiments were performed with FDW1 during growth phase (GP) in mixotrophic mode and FDW2 during stress phase (SP) in both mixotrophic and heterotrophic modes. Mixotrophic cultivation with FDW1 documented significantly higher biomass productivity (5.3g/l). Total lipid (TL) percentage was high in mixotrophic (34%) mode and neutral lipid (NL) was high in heterotrophic (13%) mode of cultivation during SP with FDW2. Overall, the microalgae growth is favoured with effluents containing high acetate, and low butyrate concentrations. Mixotrophic cultivation enhanced both biomass growth and lipid production along with simultaneous treatment.