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The bioremediation of digestate using microalgae presents a solution to the current eutrophication issue in Northwest Europe, where the use of digestate as soil fertiliser is limited, thus resulting in an excess of digestate. Ammonium is the main nutrient of interest in digestate for microalgal cultivation, and improving its availability and consequent uptake is crucial for optimal bioremediation. This work aimed to determine the influence of pH on ammonium availability in cultures of two green microalgae, additionally screened for their growth performances on three digestates produced from different feedstocks, demonstrating the importance of tailoring a microalgal strain and digestate for bioremediation purposes. Results showed that an acidic pH of 6–6.5 resulted in a better ammonium availability in the digestate media, translated into better growth yields for both S. obliquus (GR: 0.099 ± 0.001 day⁻¹; DW: 0.23 ± 0.02 g L⁻¹) and C. vulgaris (GR: 0.09 ± 0.001 day⁻¹; DW: 0.49 ± 0.012 g L⁻¹). This result was especially true when considering larger-scale applications where ammonium loss via evaporation should be avoided. The results also demonstrated that digestates from different feedstocks resulted in different growth yields and biomass composition, especially fatty acids, for which, a digestate produced from pig manure resulted in acid contents of 6.94 ± 0.033% DW and 4.91 ± 0.3% DW in S. obliquus and C. vulgaris, respectively. Finally, this work demonstrated that the acclimation of microalgae to novel nutrient sources should be carefully considered, as it could convey significant advantages in terms of biomass composition, especially fatty acids …