Peltier cooling systems are usually smaller, more portable, and relatively simpler to operate compared to conventional vapor compression cooling systems. For this reason, Peltier cooling systems are widely recommended for use in the field of cooling applications and refrigerators. These cooling systems have relatively low efficiency despite extensive operation. To solve this problem, a Peltier cooling system operated with advanced nanofluid is proposed in this study. In this cooling system, water-based Fe3O4 nanofluids were used to cool the Peltier. In order to obtain high stability in these nanofluids, the nanoparticles were synthesized chemically with surface modification processes (Fe3O4@SiO2@(CH2)3IM). By designing and manufacturing an air-to-nanofluid cooling system, the performance of Peltier cooling system was evaluated and compared to the conventional air-to-water system. The nanofluids were prepared in three different volume concentrations as 0.2%, 0.5% and 1.0% and then were examined at different working conditions. This research has been analyzed using both experimental and numerical methods. Temperature measurements and experimental COP evaluations were made in the cooling chamber. The flow structure and temperature distribution in spiral heat exchanger were closely surveyed and discussed in detail. According to the results obtained, nanofluid volumetric concentrations, inlet temperatures and mass flow rates had a significant effect on the cooling performance of the Peltier systems. It was observed that COP values decreased over time in all experiments and approach zero gradually.