Microalgae-bacteria biomass was digested through anaerobic digestion (AD) to produce biogas. Since microalgae typically have a more resistant cell wall than activated sludge (AS), its anaerobic biodegradability is limited. Therefore, three different pre-treatment techniques were evaluated for their effect on anaerobic biodegradability, especially of the extracellular polymeric substances (EPS). Firstly, heat at 70 °C for 1.5 h. Secondly, exposure to a mixture of commercially available enzymes (cellulase, α-amylase and protease), and thirdly, adding crude hydrolytic enzymes extracted by ultrasonication from a highly loaded anaerobic digestion cascade reactor. The first and third treatments had better effects than enzymatic pre-treatment with commercial enzymes, improving anaerobic biodegradability, the solubilisation of organic matter and increasing the methane production rate by 78 and 21 %, respectively. The EPS content of microalgae-bacteria biomass was considerably lower than reported for WAS, and about 40–50 % of the EPS consisted of proteins and polysaccharides. The hydrolysis of proteins and polysaccharides was quantified, and its effect on AD was discussed. A COD balance showed that the increase of soluble COD is due to the conversion of tightly bound EPS into loosely bound and soluble EPS but also due to the release of organic matter from cellular material. Although all pre-treatments increased the soluble organic fractions, especially those corresponding to EPS, none significantly improved the overall methane yield. Nevertheless, the methane production rate increased after thermal and pre-treatment with hydrolytic enzymes, which could result in smaller and more efficient anaerobic reactors.