In this study, the effects of Microbial Carbonate Precipitation (MCP), on physical and mechanical properties of Cold Asphalt Emulsion Mixtures (CAEMs) have been investigated. MCP method was performed on CAEMs by two scenarios: (I) Bio-deposition treatment of aggregates and, (II) using a medium culture containing bacteria and urea-CaCl2 nutrient solution as a replacement for optimum water content, in the manufacturing process. Additionally, in the second scenario, the effect of different curing durations (7, 14, 28 and 56 days) on the mixtures' properties has been examined. In order to ensure the formation of CaCO3 precipitation on the aggregates (first scenario), X-Ray Diffraction and Fourier-Transform Infrared Spectroscopy tests were used. Atomic Force Microscopy and FE-SEM technique were also employed to evaluate the micro-roughness of aggregates' surface and the effect of MCP on the structure of CAEMs, respectively. Ultrasonic Pulse Velocity, Indirect Tensile Strength and Semi-Circular Bending tests were performed to investigate the mechanical properties of the CAEMs. In order to assess the significance of the tests' results, analysis of variance (ANOVA) was done at 95% confidence level. Results indicated that the CaCO3 precipitations are formed on the aggregates, and also, the roughness is increased on the surface of treated aggregates. The weight increase in samples fabricated by both treatment scenarios was confirmed the formation of CaCO3 precipitations, as well. The CAEMs of first scenario revealed significantly higher dynamic modulus, indirect tensile strength, fracture energy and resistance to crack propagation, compared with the control mixtures. Significant improvements were also observed in the mechanical properties of CAEMs of second scenario after 28 days of curing, but this improvement is still lower than that of the CAEMs of first scenario. Findings revealed that MCP method can significantly improve the mechanical properties of cold asphalt mixtures. But, it doesn't significantly affect their physical properties.