Background: Bacillus cereus and Yersinia enterocolitica are implicated in foodborne diseases that have major effects on human health; therefore, it is considered universal public health disorders. Essential oils and essential oils nano emulsions have a sufficient antibacterial performance against a variety of bacteria, especially multi-drug resistant bacteria. Probiotics showed several health benefits via moderating the GIT microbiota and their metabolites. Aim: The study was designed to evaluate the biocontrol ability of cinnamon essential oil (CEO) nano emulsion and probiotics as natural antibacterial additives and reveal their bactericidal mechanism. Methods: 250 random samples (50 raw milk, 50 rice pudding, 50 kariesh cheese, 50 yogurt, and 50 ice cream) were purchased separately from different areas in Mansoura city, Egypt, and exposed to bacteriological analysis. Results: Bacillus cereus was found with the highest mean value of 66 × 107 ± 1.3 × 108 CFU/g in raw milk and the lowest mean value of 28 × 107 ± 2.6 × 107 CFU/g in kariesh cheese while Y. enterocolitica was found in 64% of the total inspected samples with the highest incidence (84%) in yogurt. The toxinogenic potential of the tested pathogens has been evaluated by multiplex PCR pointing nhe A and ces genes for B. cereus isolates while targeting in Y. enterocolitica 16s rRNA, and YST gene. Different concentrations (0.17%, 0.25%, 0.5%, 0.8%, 1%, 1.5%, and 2%) of cinnamon oil nano emulsion were employed in this study. CEO nano emulsion had the highest reduction rate at a concentration of 1.5% in the case of B. cereus and 2% in the case of Y. enterocolitica. Among different types of probiotics, the best one which showed inhibitory potential against B. cereus and Y. enterocolitica was L. plantarum. Conclusion: Lactobacillus plantarum and CEO nano emulsion at a concentration of 2% have the highest reduction rate against Y. enterocolitica, while L. plantarum and CEO nano emulsion at a concentration of 1.5% has the best antibacterial effect against B. cereus. In conclusion, more attention is required for both safety and quality in dairy products through the application of natural additives such as essential oils and probiotics.