Poultry litter extract (PLE) was treated using a microbial consortium dominated by the filamentous cyanobacterium Leptolyngbya sp. in synergy with heterotrophic microorganisms of the poultry waste. Laboratory- and pilot-scale experiments were conducted under aerobic conditions using suspended and attached growth photobioreactors. Different dilutions of the extract were performed, leading to different initial pollutant (nitrogen, phosphorus, dissolved chemical oxygen demand (d-COD), total sugars) concentrations. Significant nutrient removal rates, biomass productivity, and maximum lipid production were determined for all the systems examined. Higher d-COD, nitrogen, phosphorus, and total sugars removal were recorded in the attached growth reactors in both laboratory- (up to 94.0%, 88.2%, 97.4%, and 79.3%, respectively) and pilot-scale experiments (up to 82.0%, 69.4%, 81.0%, and 83.8%, respectively). High total biomass productivities were also recorded in the pilot-scale attached growth experiments (up to 335.3 mg L−1d−1). The produced biomass contained up to 19.6% lipids (w/w) on a dry weight basis, while the saturated and monounsaturated fatty acids accounted for more than 70% of the total fatty acids, indicating a potential biodiesel production system. We conclude that the processing systems developed in this work can efficiently treat PLE and simultaneously produce lipids suitable as feedstock in the biodiesel manufacture.