Wastes generated during the cultivation of marine microalga Crypthecodinium cohnii and after the lipid extraction process, were energetically valorized into biogas production through anaerobic digestion (AD). The tested wastes were extracted microalgae (Ae) with hexane (AeH) using supercritical extraction methods (AeS) and the supernatant obtained after culture medium centrifugation (M). The digestion of the algae biomass in the admixture with the supernatant medium (AeH+M+I and AeS+M+I) provided a higher methane content and a higher methane yield (582 and 440 L CH4/kg VS) than the substrates Ae and M, individually digested (155 and 96 L CH4/kg VS, respectively). Flow cytometry monitoring processes during AD indicated that the yield of the accumulated biogas was influenced by the operating conditions. The mixture of AeH+M+I was the only assay with a proportion of cells with less damaged membranes after AD, providing the highest methane yield and productivity (582 L CH4/kg VS and 31 L CH4/kg VS.d, respectively) and the highest energetic potential of 5.8 KWh/kg VS of all the substrates. From the results, AD integration to lipid production by C. cohnii to recover energy from the generated wastes enhanced the sustainability of the entire process and promoted the practice of zero waste.