Tertiary wastewater treatment with microalgae incorporates environmental sustainability with future technologies and high exploitation costs. Despite the apparent ecological benefits of microalgae-assisted wastewater treatment/biomass-based resource production, technological improvements are still essential to compete with other technologies. Bio-flocculation instead of mechanical harvesting has been demonstrated as an alternative cost-effective approach. So far, mostly filamentous fungi of genus Aspergillus have been used for this purpose. Within this study, we demonstrate a novel approach of using white-rot fungi, with especially high potential of algae—Irpex lacteus complex that demonstrates efficiency with various microalgae species at a broad range of temperatures (5–20 °C) and various pH levels. Harvesting of microalgae from primary and secondary wastewater resulted in 73–93% removal efficiencies within the first 24 h and up to 95% after 48 h. The apparent reuse potential of the algae—I. lacteus pellets further complements the reduced operating costs and environmental sustainability of bio-flocculation technology.