Around 29 million tons of milk end as waste yearly in Europe, representing an environmental issue but also a potential substrate for biological valorization given its nutritional value. Aspergillus oryzae and Neurospora intermedia are edible filamentous fungi with dissimilar metabolism when grown in expired milk. Neurospora intermedia is more devoted to lactose consumption; 68 and 57% of lactose was consumed after cultivation in expired milk and its liquid fraction, respectively. Aspergillus oryzae consumed less lactose in expired milk (14%), but led to better microfiltration characteristics of the final effluent due to fat and protein degradation. A two-stage fed-batch cultivation using membrane bioreactors (MBRs) was developed, bringing together both fungal metabolic characteristics when grown in 70% diluted expired milk. In the first MBR, A.oryzae degraded fat and protein, improved microfiltration, and produced ca 11 g/L of biomass. In the second MBR, N. intermedia consumed the remaining lactose in the permeate and originated ca 7 g/L of biomass. The developed system was successful for valorization of non-sterile milk due to the balance between consumption of bacterial growth-derived acids, consequent pH, and fungal enzymatic activities. Besides, a final clear effluent (83% reduction of COD) was obtained, which is of interest considering wastewater treatment.