In this study a natural mix of microalgae grown in wastewater of municipal character was co-digested with sewage sludge in mesophilic conditions, in both batch and semi-continuous modes. The semi-continuous experiment was divided into two periods with OLR1 (organic loading rate) of 2.4 kg volatile solids (VS) m−3 d−1 and HRT1 (hydraulic retention time) of 15 days, and OLR2 of 3.5 kg VS m−3 d−1 and HRT2 of 10 days, respectively. Results showed stable conditions during both periods. The methane yield was reduced when adding microalgae (from 200 ± 25 NmL CH4 g VSin−1, to 168 ± 22 NmL CH4 g VSin−1) but VS reduction was also decreased by 51%. This low digestibility was confirmed in the anaerobic batch test. However, adding microalgae improved the dewaterability of the digested sludge. The high heavy metals content in the microalgae resulted in a high heavy metals content in the digestate, making it more difficult to reuse the digestate as fertilizer on arable land. The heavy metals are thought to originate from the flue gas used as a CO2 source during the microalgae cultivation. Therefore the implementation of CO2 mitigation via algal cultivation requires careful consideration regarding the source of the CO2-rich gas.