Microalgae have been recently recognized as a promising alternative for the effective treatment of anaerobic digestion effluents. However, to date, a widely applied microalgae-based process is still absent, due to several constraints mainly attributed to high ammonia concentrations and turbidity, both hindering microalgal growth. Within this scope, the purpose of the present study was to investigate the performance of two Chlorella strains, SAG 211-11b and a local Algerian isolate, under different nitrogen levels, upon ammonia stripping. The experiments were performed on cylindrical photobioreactors under controlled pH (7.8 ± 0.2) and temperature (25 ± 2 °C). Cultures were monitored for biomass production and substrate consumption. After sampling at the beginning of the stationary phase of growth (12th day) and after the maturation of the cells (24th day), an analysis of the produced biomass was conducted, in terms of its biochemical components. The local isolate grew better than C. vulgaris 211-11b, resulting in 1.43 mg L⁻¹ biomass compared to 1.02 mg L⁻¹ under 25 mg NH₄-N L⁻¹, while organic carbon and nutrient consumption varied between the two strains and different conditions. Concerning biomass quality, a high initial NH₄-N concentration led to high protein content, while low nitrogen levels favored fatty acid (FA) accumulation, though the production of pigments was inhibited. In particular, the protein content of the final biomass was determined close to 45% of the dry weight in all experimental scenarios with adequate nitrogen, while proteins decreased, and the fatty acids approached 20% in the case of the local isolate grown on the substrate with the lowest initial ammonium nitrogen (25 mg NH₄-N L⁻¹). The novelty of the present work lies in the comparison of a microalga with industrial applications against a local isolate of the same species, which may prove to be even more robust and profitable.