Photosynthetic microbial fuel cells (pMFCs) are hybrid systems that enable simultaneous wastewater treatment under anaerobic conditions and the generation of electricity by utilizing the potential difference in the anaerobic anode chamber and the oxygenated cathode chamber. Dairy wastewater with a concentration of 2000 mg COD/L was treated in the anode of a batch pMFC. In the cathode chamber, Chlorella vulgaris or Arthrospira platensis was cultivated in synthetic medium, and next in diluted effluent from the anode chamber. The highest power density of 91 mW/m2 was generated by the pMFC with the cultivation of Arthrospira platensis. Higher values of dissolved oxygen remained during the dark phase in the cathodic medium with Arthrospira platensis cultivation than with Chlorella vulgaris. This depletion of oxygen significantly decreased voltage generation, which during the light phase increased again to the maximum values. The COD removal achieved in the anodic chamber was 87%. The efficiency of nitrogen removal in the cathode chamber during the cultivation of Arthrospira platensis and Chlorella vulgaris was about 78% and 69%, respectively. The efficiency of phosphorus removal in the cathode chamber with the cultivation of Arthrospira plantensis and Chlorella vulgaris was 58% and 43%, respectively. This study has shown that the introduction of Arthrospira platensis into the cathode chamber is more effective than that of Chlorella vulgaris.