The milk’s natural flora, or the starter, can preserve cheesemaking and allow for microbial competition. This investigation aimed to improve cheese safety and assess its characteristics using probiotic cell pellets (LCP) or cell-free extracts (CFS). Cheese samples were collected from different areas to investigate the current contamination situation. Six CFSs of probiotics were assessed as antifungal against toxigenic fungi using liquid and solid media and their aflatoxin reduction impact. The most effective CFS was chosen for cheese coating in nanoemulsion. Coated cheese with CFS, LCP, and LCP-CFS was assessed against control for changes in chemical composition, ripening indications, rheological properties, and microbiology. Results showed significant contamination levels in the collected samples, and toxic fungi were present. Lactobacillus rhamnosus CFS has aflatoxins reducibility in liquid media. During cheese ripening, uncoated cheese showed higher fat, protein, salt content, soluble nitrogen, total volatile fatty acids, tyrosine, and tryptophan contents than coated samples, except for LCP-coating treatment. Cheese rheology indicated that coating treatments had the lowest hardness, cohesiveness, gumminess, chewiness, and springiness compared to uncoated cheese. Uncoated cheese had the highest yeast and mold counts compared to the treated ones. The LCP-CFS-coated cheese showed no Aspergillus cells for up to 40 days. Uncoated Ras cheese recorded slightly lower flavor, body, texture, and appearance scores than coated cheeses. In conclusion, coating cheese with L. rhamnosus nanoemulsion has antifungal and antiaflatoxigenic properties, even for LCP, CFS, and CFS-LCP, which could extend cheese shelf life.