Display omitted •The nitrogen stress affects morphology and biochemical composition of microalgae.•Scenedesmus sp. is able to grow at 80% reduction in nitrate compared to BG-11.•Complete nitrate starvation gives 45.74% carbohydrate & 27.93% lipid accumulation.•Scenedesmus sp. is a potential feed stock for biodiesel and bio-ethanol production.•De-oiled biomass of Scenedesmus sp. can be used for bio-ethanol production. The aim of present study was to investigate the effects of nitrogen limitation as well as sequential nitrogen starvation on morphological and biochemical changes in Scenedesmus sp. CCNM 1077. The results revealed that the nitrogen limitation and sequential nitrogen starvation conditions significantly decreases the photosynthetic activity as well as crude protein content in the organism, while dry cell weight and biomass productivity are largely unaffected up to nitrate concentration of about 30.87mg/L and 3days nitrate limitation condition. Nitrate stress was found to have a significant effect on cell morphology of Scenedesmus sp. CCNM 1077. Total removal of nitrate from the growth medium resulted in highest lipid (27.93%) and carbohydrate content (45.74%), making it a potential feed stock for biodiesel and bio-ethanol production. This is a unique approach to understand morphological and biochemical changes in freshwater microalgae under nitrate limitation as well as sequential nitrate removal conditions.