This work investigates the influence of using microbial coagulants, including Rhizomucor miehei (MCR) protease and Cryphonectria parasitica (MCC) protease, on the quality characteristics of low-fat Edam cheese made from ultrafiltered buffalo milk (LFUE). Concurrently, a benchmark with calf rennet (CR) has been also performed. Throughout a 90-day ripening period, the cheeses were assessed for their physicochemical features, proteolysis, texture, free amino acid and free fatty acid content, microstructure, and sensory attributes. The study revealed that both microbial coagulants had no significant impact on the physicochemical composition and firmness of the cheeses while slightly affected the free fatty acids. Cheeses made with microbial coagulants displayed higher proteolysis, with MCR and MCC cheeses exhibiting greater levels of water-soluble nitrogen and 12% trichloroacetic acid-soluble nitrogen than CR cheese. MCR and MCC cheeses exhibited more extensive breakdown of αs- and β-caseins, as indicated by the SDS-PAGE electrophoretogram, compared to CR cheese during ripening. As for the proteolytic activity, the microbial coagulant contributed to shaping the free amino acid content, microstructure, and sensory qualities of the cheeses. Notably, MCC cheese outperformed MCR or CR cheeses in terms of free amino acid levels. MCR and MCC cheeses resulted in smooth microstructures with uniform protein networks as observed by microscopy, while CR cheese displayed rough, granular surfaces. With the highest scores for appearance, body, texture, and flavor, MCC cheese demonstrated superior sensory properties compared with MCR and CR cheeses.