Microalgae harbor a not fully exploited industrial and environmental potential due to their high metabolic plasticity. In this context, a better understanding of the metabolism of microalgae and microalgal-bacterial consortia under stress conditions is essential to optimize any waste-to-value approach for their mass cultivation. This work constitutes a fundamental study of the mixotrophic metabolism under stress conditions of an axenic culture of Chlorella sorokiniana and a microalgal-bacterial consortium using carbon, nitrogen, and phosphorous mass balances. The hydrolysis of glucose into volatile fatty acids (VFA) during dark periods occurred only in microalgal-bacterial cultures and resulted in organic carbon removals in the subsequent illuminated periods higher than in C. sorokiniana cultures, which highlighted the symbiotic role of bacterial metabolism. Acetic acid was preferentially assimilated over glucose and inorganic carbon by C. sorokiniana and by the microalgal-bacterial consortium during light periods. N-NH4 (+) and P-PO4 (-3) removals in the light stages decreased at decreasing duration of the dark stages, which suggested that N and P assimilation in microalgal-bacterial cultures was proportional to the carbon available as VFA to produce new biomass. Unlike microalgal-bacterial cultures, C. sorokiniana released P-PO4 (-3) under anaerobic conditions, but this excretion was not related to polyhydroxybutyrate accumulation. Finally, while no changes were observed in the carbohydrate, lipid and protein content during repeated extended dark-light periods, nutrient deprivation boosted both C-acetate and C-glucose assimilation and resulted in significantly high biomass productivities and carbohydrate contents in both C. sorokiniana and the microalgal-bacterial cultures.