A mix of microalgae and bacteria was cultivated on pre-sedimented municipal wastewater in a continuous operated microalgae-activated sludge process. The excess material from the process was co-digested with primary sludge in mesophilic and thermophilic conditions in semi-continuous mode (5 L digesters). Two reference digesters (5 L digesters) fed with waste-activated sludge (WAS) and primary sludge were operated in parallel. The methane yield was slightly reduced (≈10%) when the microalgal-bacterial substrate was used in place of the WAS in thermophilic conditions, but remained approximately similar in mesophilic conditions. The uptake of heavy metals was higher with the microalgal-bacterial substrate in comparison to the WAS, which resulted in higher levels of heavy metals in the digestates. The addition of microalgal-bacterial substrate enhanced the dewaterability in thermophilic conditions. Finally, excess heat can be recovered in both mesophilic and thermophilic conditions.