Anaerobic methane generation from algae is hindered by the slow and poor algae biodegradability. A novel free ammonia (NH3 i.e. FA) pretreatment technology was proposed in this work to enhance anaerobic methane generation from algae cultivated using a real secondary effluent. The algae solubilisation was 0.05–0.06 g SCOD/g TCOD (SCOD: soluble chemical oxygen demand; TCOD: total chemical oxygen demand) following FA pretreatment of 240–530 mg NH3–N/L for 24 h, whereas the solubilisation was only 0.01 g SCOD/g TCOD for the untreated algae. This indicates that FA pretreatment at 240–530 mg NH3–N/L could substantially enhance algae solubilisation. Biochemical methane potential tests revealed that FA pretreatment on algae at 240–530 mg NH3–N/L is able to significantly enhance anaerobic methane generation. The hydrolysis rate (k) and biochemical methane potential (P0) of algae increased from 0.21 d−1 and 132 L CH4/kg TCOD to 0.33–0.50 d−1 and 140–154 L CH4/kg TCOD, respectively, after the algae was pretreated by FA at 240–530 mg NH3–N/L. Further analysis indicated that FA pretreatment improved k of both quickly and slowly biodegradable substrates, and also increased P0 of the slowly biodegradable substrate although it negatively affected P0 of the quickly biodegradable substrate. This FA technology is a closed-loop technology.