Presence of urine in municipal wastewater is a major problem faced by wastewater treatment plants. The adverse effects are noticeable as crystallization in equipment and pipelines due to high concentration of nitrogen and phosphorus. Therefore, improved technologies are required that can treat urine separately at the source of their origin and then discharge it in the main wastewater stream. In this study, the performance of the microbial fuel cell (MFC) was evaluated with mixed consortia and isolated pure cultures (Firmicutes and Proteobacter species) from biofilm for electricity generation and nutrient recovery. Microbes utilize less than 10% of total phosphorus for their growth, while 90% is recovered as struvite. The amount of struvite recovered was similar for pure and mixed culture (12 ± 5 g/L). The microbial characterization also shows that not all the biofilm-forming bacterial isolates are very much efficient in power generation and, hence, they can be further exploited to study their individual role in operating MFC. The different organic loading rates experiment shows that the performance of MFC in terms of power generation is the same for undiluted and five times diluted urine while the recovery of nutrients is better with undiluted urine, implying its direct use of urine in operating fuel cell.