Integrated photo-bioelectrochemical (IPB) systems are a newly emerging technology for sustainable wastewater treatment through synergistic cooperation between microbial fuel cells (MFCs) and algal bioreactors. This study aimed to advance our understanding of the IPB performance in contaminant removal and bioenergy production and how IPB function is affected by different algal–bacterial inocula. Fed with a synthetic solution, the IPB system could achieve more than 90% removal of solution organic compounds and nearly 100% of ammonium nitrogen. Production of algal biomass was significantly different among three inocula, varying from 5.9 to 53.3mgL−1. The highest energy production was 0.089kWhm−3, including direct electrical energy of 0.055kWhm−3 and indirect electrical energy of 0.034kWhm−3 from biomass conversion, and a positive energy balance could be achieved. The natural algal inocula resulted in the cyanobacteria Leptolyngbya and green alga Acutodesmus as dominant photoautotrophs in cathode suspension and biofilms, providing oxygen for MFC function. Differences in IPB efficiency could be related to microbial composition; one inoculum resulted in absence of Xanthomonadaceae bacteria, while another had more γ-proteobacteria. Specific taxa identified could be important for optimizing electricity generation and algal biomass for biofuel production.