Microalgae grown in swine wastewater were used as a promising strategy to produce renewable energy by coupling wastewater bioremediation and biomass revalorization. The efficiency of a microalgae consortium treating swine slurry at different temperature (15 and 23 °C) and illumination periods (11 and 14 h) was assessed for biomass growth and nutrient removal at two NH4+ initial concentrations (80 and 250 mg L−1 NH4+). Favourable culture conditions (23 °C and 14 h of illumination) and high ammonium loads resulted in higher biomass production and greater nutrients removal rates. The initial N–NH4+ load determined the removal mechanism, thus ammonia stripping and nitrogen uptake accounted similarly in the case of high NH4+ load, while nitrogen uptake prevailed at low NH4+ load. Under favourable conditions, nitrogen availability in the media determined the composition of the biomass. In this context, carbohydrate-rich biomass was obtained in batch mode while semi-continuous operation resulted in protein-rich biomass. The revalorization of the resultant biomass was evaluated for biogas production. Methane yields in the range of 106–146 and 171 ml CH4 g COD−1 were obtained for the biomasses grown in batch and semi-continuous mode, respectively. Biomass grown under favourable conditions resulted in higher methane yields and closer to the theoretically achievable.