The algae-based technology has a positive effect on the treatment of biogas slurry and the purification of biogas, while vitamin B12 (VB12) is one of the important regulatory substances in the algae-based cultivation system. In this study, different concentrations of VB12 were used in three microalgal treatment technologies to assess their effect on simultaneous removal of nutrients from biogas slurry and removal of CO2 from raw biogas. Results showed that Chlorella vulgaris exhibited higher growth rate, mean daily productivity, chlorophyll a content, carbonic anhydrase activity and better photosynthetic properties when co-cultivated with Ganoderma lucidum, rather than when co-cultivated with activated sludge or under mono-cultivation. Maximum mean chemical oxygen demand, total nitrogen, total phosphorus and CO2 removal efficiencies were found to be 84.29 ± 8.28%, 83.27 ± 8.14%, 85.27 ± 8.46% and 65.71 ± 6.35%, respectively when microalgae were co-cultivated with Ganoderma lucidum under 100 ng L-1 of VB12. This study shows the potential of microalgae and fungi co-cultivation supplemented with VB12 for the simultaneous upgradation of biogas production as well as for the purification of biogas slurry.