Using whey, a by-product of the cheese-making process, is important for maximizing resource efficiency and promoting sustainable practices in the food industry. Reusing whey can help minimize environmental impact and produce bio-preservatives for foods with high bacterial loads, such as Mexican-style fresh cheeses. This research aims to evaluate the antimicrobial and physicochemical effect of CFS from Lactobacillus casei 21/1 produced in a conventional culture medium (MRS broth) and another medium using whey (WB medium) when applied in Mexican-style fresh cheese inoculated with several indicator bacteria (Escherichia coli, Salmonella enterica serovar Typhimurium, Staphylococcus aureus, and Listeria monocytogenes). The CFSs (MRS or WB) were characterized for organic acids concentration, pH, and titratable acidity. By surface spreading, CFSs were tested on indicator bacteria inoculated in fresh cheese. Microbial counts were performed on inoculated cheeses during and after seven days of storage at 4 ± 1.0 °C. Moreover, pH and color were determined in cheeses with CFS treatment. Lactic and acetic acid were identified as the primary antimicrobial metabolites produced by the Lb. casei 21/1 fermentation in the food application. A longer storage time (7 days) led to significant reductions (p < 0.05) in the microbial population of the indicator bacteria inoculated in the cheese when it was treated with the CFSs (MRS or WB). S. enterica serovar Typhimurium was the most sensitive bacteria, decreasing 1.60 ± 0.04 log10 CFU/g with MRS-CFS, whereas WB-CFS reduced the microbial population of L. monocytogenes to 1.67 log10 CFU/g. E. coli and S. aureus were the most resistant at the end of storage. The cheese's pH with CFSs (MRS or WB) showed a significant reduction (p < 0.05) after CFS treatment, while the application of WB-CFS did not show greater differences in color (ΔE) compared with MRS-CFS. This study highlights the potential of CFS from Lb. casei 21/1 in the WB medium as an ecological bio-preservative for Mexican-style fresh cheese, aligning with the objectives of sustainable food production and guaranteeing food safety.