This study investigated the production of rennet gels from β-casein-depleted retentates obtained through cold microfiltration (MF) of skim milk (SM) that was treated beforehand to ensure microbial safety. The treatments included thermization (65 °C, 20 s), pasteurization (72 °C, 15 s), and microfiltration (50 °C; 1.4 μm pore size). The reduction in β-casein content was 0.98, 0.51 and 0.90%, respectively. All treatments resulted in the partial aggregation of serum proteins, which were slightly concentrated in the retentates obtained post cold MF process. This aggregation, along with concentration effect, likely inhibited β-casein dissociation from casein micelles and permeation, particularly in pasteurized milk. Renneting and coagulation properties of the retentates were comparable to those of the respective SM samples, with no significant differences in syneresis, water-holding capacity, or protein hydration. Notably, the retentate from thermized SM, which showed the best performance with the highest β-casein reduction (0.98%), demonstrated shorter coagulation time compared to retentate from pasteurized milk or the corresponding unfiltered SM. Textural analysis revealed greater firmness, cohesiveness, and viscosity of retentate-based rennet gels compared to gels made from unfiltered SM, attributed to protein concentration during cold MF. Overall, this study successfully produced rennet gels from cold MF retentates without compromising their physicochemical properties.