► Two agroindustrial wastewaters are used as culture medium for microalgae production. ► Phosphorous limitation triggers lipid accumulation in produced biomass. ► Anaerobic batch experiments are carried out using the produced biomass. ► Lower TCOD/VS ratio (0.5) promotes higher methane yield. ► The higher lipid content (30%), the higher methane yield. Two combined processes were studied in order to produce second generation biofuels: microalgae biomass production and its further use to produce biogas. Two 5L photobioreactors for treating wastewater from a potato processing industry (from now on RPP) and from a treated liquid fraction of pig manure (from now on RTE) were inoculated with Chlorella sorokiniana and aerobic bacteria at 24±2.7°C and 6000lux for 12h per day of light supply. The maximum biomass growth was obtained for RTE wastewater, with 26.30mg dry weightL−1d−1. Regarding macromolecular composition of collected biomass, lipid concentration reached 30.20% in RPP and 4.30% in RTE. Anaerobic digestion results showed that methane yield was highly influenced by substrate/inoculum ratio and by lipids concentration of the biomass, with a maximum methane yield of 518mL CH4 g COD−1added using biomass with a lipid content of 30% and a substrate/inoculum ratio of 0.5.