Increasing energy demands and greenhouse gases emission from wastewater treatment processes prompted the investigation of alternatives capable to achieve effective treatment, energy and materials recovery, and reduce environmental footprint. Combination of microbial fuel cell (MFC) technology with microalgal-based process in MFC-PBR (photobioreactor) systems could reduce greenhouse gases emissions from wastewater treatment facilities, capturing CO2 emitted from industrial facilities or directly from the atmosphere. Microalgae production could enhance recovery of wastewater-embedded resources. Two system MFC-PBR configurations were tested and compared with a control MFC, under different operating conditions, using both synthetic and agro-industrial wastewater as anolytes. COD removal efficiency (ηCOD) and energy production were monitored during every condition tested, reaching ηCOD values up to 99%. Energy recovery efficiency and energy losses were also evaluated. The system equipped with microalgal biocathode proved to be capable to efficiently treat real wastewater, surpassing the effectiveness of the control unit under specific conditions. Oxygen provided by the algae improves the overall energy balance of this system, which could be further enhanced by many possible resources recovery opportunities presented by post-processing of the cathodic effluent.