There is great controversy regarding the best substrate (fresh or anaerobically digested swine slurry) for the development of microalgae-bacteria consortia. This study aims to elucidate the best substrate by assessing biomass productivity, microorganism predominance, and their ability for organic matter removal. In addition to the different substrates, different operational conditions and influent strengths were evaluated. Increasing organic matter content when favourable temperature and illumination conditions were present improved biomass production. However, these conditions were not favourable for microalgal growth, but they were favourable for bacteria. Regardless of the operational conditions, reactors fed with fresh slurry not only resulted in the highest biomass productivity, but also the greatest removal of total and soluble chemical oxygen demand (COD). On the other hand, reactors fed with digested slurry showed biomass productivity and COD removal values lower than those obtained for reactors fed with fresh slurry, most probably due to the recalcitrant nature of the former. Nevertheless, digested slurry was the substrate more appropriate for microalgae growth under harsh operational conditions (16 °C and 9-h illumination) at low influent strength and optimum operational conditions (30 °C and 24-h illumination) at higher influent strength.