MnCexFe2-xO4 (x = 0.0, 0.6, 1.4) nanoparticles were successfully synthesized via sol–gel method. Their structural and magnetic properties were studied using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and vibrating sample magnetometry techniques. The average crystallite size calculated using Scherrer equation was in the range of 26.90–60.44 nm. Scanning electron microscopy showed that the size of nanoparticles is less than 50 nm. Energy-dispersive X-ray results showed that the composition of the elements was relevant as expected from the synthesis. Vibrating sample magnetometry indicated that the samples have soft ferromagnetic properties. The highest saturation magnetization was related to the MnFe2O4 sample after annealing at 700 °C. The in vitro inhibitory activities of MnFe2O4 and MnCe1.4Fe0.6O4 nanoparticles were assessed against pathogenic fungi Aspergillus fumigatus, Candida albicans, and Fusariumoxysporum. Acceptable antifungal effects were observed in the presence of MnCe1.4Fe0.6O4 nanoparticles with minimum inhibition concentration and minimum fungicide concentration susceptibility determinations. As a result, these nanoparticles can be considered as potential antifungal agents.