Research into the development of renewable and sustainable fuels has been a major concern during last decades. Microalgae, as a potential resource, have gained great attention for energy purposes. In this context, anaerobic digestion seems to be the most direct energy generation process. Nevertheless, the efficiency of this process is hampered due to the hard cell wall of some microalgae. In order to enhance its anaerobic biodegradability, the present research investigated the effect of thermal pretreatment at two temperatures (70 and 90 °C) applied to Scenedesmus biomass. No differences were detected in terms of organic matter or ammonium release upon the two tested temperatures. Nevertheless, a different fact was observed for their anaerobic biodegradability. While raw and pretreated at 70 °C microalgae attained 22–24% anaerobic biodegradability, microalgae pretreated at 90 °C achieved anaerobic biodegradability of 48%. Even though similar profiles were obtained for both temperatures along the pretreatment period, the damage caused in the cell wall at 90 °C seemed to be greater and rendered this substrate readily degradable for anaerobic digestion. ► Efficiency of anaerobic digestion is hampered due to microalgae cell wall. ► Pretreatment temperature dependency was observed on Scenedesmus biomass. ► Sytox green dye is a helpful tool to identify cell wall disruption. ► Thermal pretreatment at 90 °C was successful for increasing methane production.