Abstract This study evaluated the enhancement of biogas production in semi-continuous anaerobic digestion fed with enzymatically pretreated Chlorella vulgaris . Organic matter in soluble phase increased from 2.5% to 45% after pretreatment with proteases. The soluble COD was easily biodegradable and almost all organic matter available in soluble phase was removed (94.4%) in the anaerobic reactor (CSTR). Methane yield increased 2.6-fold when compared to the CSTR fed with raw biomass. With regard to the nitrogen fate, 77% of the organic nitrogen was mineralized during anaerobic digestion. Slight ammonium inhibition was detected due to the high nitrogen mineralization registered. pHs remained close to neutrality throughout the experimental time. VFAs were accumulated in the last retention time as a consequence of the slight anaerobic digestion inhibition, which revealed an unbalanced equilibrium among the anaerobic microbial population. This fact was corroborated in batch digestion assays. The anaerobic sludge collected from the CSTR exhibited a different profile in terms of methane productivity when compared to the inoculum from WWTP normally used. Further studies are nowadays undertaken to overcome the inhibition and thus increase the methane yield.