Microalgae cultivation offers a sustainable approach for nutrient recovery from municipal effluents and the production of valuable biomass, although efficient harvesting remains challenging. This study evaluated the adaptation of the microalgal consortium MC-10 in a sequential batch system through reinoculation of its flocculating fraction to enhance harvesting efficiency and mineral recovery. The consortium was initially cultivated under high ionic stress to promote cell aggregation. Laboratory preadaptation using secondary municipal effluents was then conducted, followed by an outdoor evaluation. In the initial propagation stage, flocculation efficiency reached 98%. Using municipal effluents, flocculation values of 99% were obtained, with a 149% increase in flocculating biomass under laboratory conditions, and 84% flocculation with a 125% increase in biomass production under outdoor conditions, demonstrating the consortium’s stability under environmental fluctuations and its suitability for biomass harvesting. The resulting biomass showed high potential as a biofertilizer due to its mineral content (47% dry weight, DW) and acid solubility (83%), indicating high nutrient bioavailability. Additionally, it contained a total carotenoid concentration of 451 μg/g DW, adding antioxidant value. These findings support the use of microalgae cultivation for the valorization of municipal effluents through the production of easily harvestable biomass with potential for reintegration into agricultural systems.