Using anaerobic digestion (AD) to convert microalgae Scenedesmus sp. AMDD into methane represents a promising biomass-to-biofuel scenario. However, there is still a need for optimization. In this study, two pre-treatment strategies have been elaborated to obtain higher and/or faster methane yield. Microalgal biomass was hydrolyzed by a combination of enzymatic (pectate-lyase and cellulase) and thermal (121-150°C), or caustic (NaOH) and thermal (121°C) pretreatments. Pretreated microalgal biomass was fed to two Upflow Anaerobic Sludge Blanket digesters, to assess methane production at different organic loading rates (OLR) and a fixed hydraulic retention time (six days). Bacterial community was monitored using next generation sequencing technology. Both pretreatments successfully hydrolyzed up to 75% of microalgal biomass. Increasing the OLR applied to each digester yielded progressively higher methane production, as expected. The highest volumetric methane production was obtained after the caustic-thermal pretreatment, but the conversion ratio of hydrolyzed algal biomass was only marginally higher than those obtained in previous studies. A shift in the bacterial population was highlighted for both digesters, with Bacteroidetes becoming dominant in both adapted populations. Acetate-, H2/CO2- and formate-producer Syntrophus was the only emerging genus in the bacterial population after caustic-thermal pretreatment, while various VFA and H2/CO2-producers, including Syntrophus, emerged in the bacterial population after enzymatic-thermal pretreatment. The much shorter time to produce methane and the reduced footprint of the AD process in an algal biorefinery are very promising results. Identification of bacterial species particularly adapted to the bioconversion of microalgal biomass into methane will be helpful for future process optimization.