As the Greek-style yogurt market continues to experience prosperous growth, finding the most appropriate destination for yogurt acid whey (YAW) is still a challenge for Greek yogurt manufacturers. This study provides a direct alternative treatment of YAW by leveraging the abilities ofMucor circinelloidesandMucor genevensisto raise the pH of YAW and to produce fungal biomass with a high lipid content. Aerobic cultivations of these species were conducted in YAW, both with and without the addition of lactase, at 30 °C, and 200 rpm agitation. The density, pH, biochemical oxygen demand (BOD), biomass production, lipid content, fatty acid profile, and sugar and lactic acid concentrations were regularly measured throughout the 14-day cultivations. The data showed thatM. genevensiswas superior at deacidifying YAW to a pH above 6.0—the legal limit for disposing of cultured dairy waste. On the other hand,M. circinelloidesgenerated more fungal biomass, containing up to 30%w/wof lipid with high proportions of oleic acid and γ-linolenic acid. Additionally, the treatments with lactase addition showed a significant decrease in the BOD. In conclusion, our results present a viable treatment to increase the pH of YAW and decrease its BOD, meanwhile generating fungal oils that can be further transformed into biodiesel or processed into functional foods or dietary supplements.