Yeasts are common contaminants in the cheese industry, which frequently arise from raw milk, the surrounding environment, and equipment, resulting in economic losses in addition to health hazards. This study aimed to compare the antifungal effect of chitosan and nano-chitosan as natural preservatives with a commonly used chemical preservative (potassium sorbate) against Rhodotorula mucilaginosa and Candida albicans. Laboratory Karish cheese was manufactured with the addition of potassium sorbate, chitosan, nano-chitosan, and their combinations at different concentrations. The survival of R. mucilaginosa and C. albicans was monitored in different treatments (CR, PR1, PR2, CR1, CR2, NR1, NR2, MR, CC, PC1, PC2, CC1, CC2, NC1, NC2, MC) during storage in a refrigerator with continuous measurement of pH. The impact of using these antifungal agents on the organoleptic parameters of Karish cheese during storage was also evaluated. There was a significant decrease in the count of yeasts in all treatments from the 3rd day of storage, while the mixture of 0.1% potassium sorbate (MR) and 2% chitosan (MC) improved the antifungal effect of chitosan with a lower potassium sorbate concentration and showed the best antifungal effects against both R. mucilaginosa and C. albicans. This combination reduced the yeast count from 8.92 and 9.57 log10 colony-forming unit (CFU)/g in MR and MC treatments, respectively, until it became undetectable on the 9th day of storage, which was earlier than for all other treatments. It was noted that the addition of chitosan nanoparticles (ChNPs) at either 0.25% (NR1 and NC1) or 0.5% (NR2 and NC2) during the manufacturing of Karish cheese significantly lowered the counts of R. mucilaginosa and C. albicans compared with chitosan with a higher molecular weight, but significantly lower than potassium sorbate until 6th day of storage as all treatments of chitosan nanoparticles became significantly higher than potassium sorbate treatments. After 9 days of storage, NR2 and NC2 treatments showed the most significant decreases in count (3.78 and 4.93 log10 CFU/g, respectively), indicating better stability of ChNPs. At the end of the storage period, PR2, PC2, CR2, and CC2 showed significantly high pH values among the groups of 4.8, 5.0, 4.8, and 5.1, respectively. The overall acceptability was significantly higher in treated Karish cheese samples than in the control group, especially at the end of the storage period. Potassium sorbate, chitosan, and ChNPs are effective antifungal preservatives against R. mucilaginosa and C. albicans. In addition, the combination of chitosan with potassium sorbate showed synergistic antifungal activity. These additives also preserve the sensorial criteria longer than for cheese without preservatives.