Anaerobic digestion is a promising method for organic waste treatment. While the obtained digestate can function as fertilizer, the liquid fraction produced is rather problematic to discharge due to its high nitrogen and chemical oxygen demand contents. Microalgae have great potential in sustainable nutrient removal from wastewater. This study aimed at evaluating native Swedish microalgae cultivation (batch operation mode, 25°C and continuous light of 80 μmol m−2 s−1) on anaerobic digestion effluent of pulp and paper sludge (PPS) or chicken manure (CKM) to remove ammonium and volatile fatty acids (VFAs). While algal strains, Chlorella vulgaris, Chlorococcum sp., Coelastrella sp., Scotiellopsis reticulata and Desmodesmus sp., could assimilate VFAs as carbon source, acetic acid was the most preferred. Higher algal biomass and cell densities were achieved using PPS compared to CKM. In PPS, Coelastrella sp. and Chlorella vulgaris reached the highest cell densities after 15 days, about 79 × 106 and 43 × 106 cells mL−1, respectively. Although in PPS, ammonium was completely assimilated (195 mg L−1), this was only 46% (172 mg L−1) in CKM. Coelastrella sp. produced the highest biomass concentration independently of the medium (1.84 g L−1 in PPS and 1.99 g L−1 in CKM). This strain is a promising candidate for nutrient removal and biomass production in the aforementioned media, followed by Chlorella vulgaris and Chlorococcum sp. They have great potential to reduce the environmental impact of industrial anaerobic digestion effluents in Nordic countries.