Microalgae based treatment was studied to polish sequential batch reactor (SBR) treated pharmaceutical wastewater under mixotrophic mode of operation with simultaneous biomass/lipid production. At the end of biomass growth phase (BGP), carbon removal efficiency was observed to be 73% along with good removal of nitrates (62%). Since microalgae assimilate nutrients from wastewater for growth, an increment in total biomass productivity (2.8 g/l) was observed. Subjecting to nutrient stress phase (NSP), total lipid content of 17.2% with neutral lipids of 6.2% was observed under light condition. Contrarily, dark condition depicted total lipid content of 15.8% with neutral lipids constituting 6.5%. The nutrient stress in combination with light showed marked influence on the profile of saturated and unsaturated fatty acids. Integration of microalgae cultivation improves environmental sustainability and enables greener routes of biofuels and value added products synthesis in a biorefinery approach. (C) 2016 Elsevier Ltd. All rights reserved.