The use of microalgae-bacteria consortia presented high capacity to remove organic matter and nutrients from slaughterhouse wastewater. The highest biomass production (12.7 g VSS/m2 day) was achieved by biomass grown in the HRAP located in a greenhouse operating at a HRT of 10 days. This biomass had a FFA content of 142 mg FFA/g and it was the most suitable to produce biodiesel. Carbohydrates and proteins composition of microalgal biomass was affected by operational conditions. The highest CH4 yield was achieved by lipid exhausted biomass, evidencing that SCCO2 extraction increases biodegradability for further biogas production, increasing the economic viability.