Concentrated animals feeding operations (CAFOs) often pose a negative environmental impact due to the uncontrolled spreading of manure into soils that ends up in the release of organic matter and nutrients into water bodies. Conventional aerobic methods treating CAFOs wastewater require intensive oxygenation, which significantly increases the operational costs. The alternative proposed in this research is the application of micro-algae based systems by taking advantage of the cost-effective in situ oxygenation via photosynthesis. A 4.9 L enclosed tubular biofilm photo-bioreactor was inoculated with an algal–bacterial consortium formed by the micro-algae Chlorella sorokiniana and a mixed bacterial culture from an activated sludge process. C. sorokiniana delivers the O2 necessary to accomplish both organic matter and ammoniun oxidation. The reactor was fed with diluted swine wastewater containing 180, 15 and 2,000 mg/L of NH4+-N, soluble P and total COD, respectively. The photo-bioreactor exhibited good and sustained nutrient removal efficiencies (up to 99% and 86% for NH4+ and PO43−, respectively) while total COD was removed up to 75% when the biofilm was properly established. Liquid superficial velocities up to 0.4 m/s (achieved by culture broth recirculation) hindered the formation of a stable biofilm, while operation at velocities lower than 0.1 m/s supported stable process performance. The high shear stress imposed by the centrifugal recirculation pump disintegrated the large aggregates detached from the biofilm, which resulted in a poor settling performance and therefore poor COD removal efficiencies. Enclosed biofilm photo-bioreactors therefore offer a potentially more economical alternative to conventional tertiary treatments process.