The cultivation of microalgae with digestate supernatant is a promising process for the recovery of mineralized nutrients (P, N) from anaerobic digestion. Nevertheless, the variability of phosphorus concentration in the influent could limit this process. The impact of initial N:P ratios between 3 and 76 gN gP−1 was studied and proved no growth limitation over 14-day batch experiments even when P was depleted. Nitrogen assimilation was not affected by phosphorus concentrations and reached 10.1 mgN L−1 d−1 whereas phosphorus removal ranged from 0.6 to 2.0 mgP L−1 d−1. The biomass N:P ratio was found to be a function of the influent N:P ratio. Phosphorus storage by microalgae was thus confirmed. Nitrification was found to be highly dependent on the initial phosphorus concentration. The evolution of microalgae communities was also monitored and revealed the advantage of Scenedesmus over Chlorella when the media was phosphorus-depleted.