Bacillus cereus is one of the foodborne pathogens that is incriminated in several outbreaks worldwide. The objectives of the current study were first to determine the prevalence of B. cereus-contaminated milk and dairy products retailed in Egypt. Secondly, the antimicrobial resistance profiling and virulence-associated genes of the recovered B. cereus isolates were assessed. Finally, natural and eco-friendly natural additives such as D-tryptophan and L-ascorbic acid were used for controlling the viability of Bacillus cereus spores. A total of 200 samples including market raw milk, Ultra-Heat Treated (UHT) milk, Kariesh cheese, soft white cheese (Damietta), and rice pudding, 50 of each were examined. The results of our study indicated that 31% of the examined dairy samples were contaminated with B. cereus. Surprisingly, 90% of the isolates showed multidrug-resistance against ampicillin, amoxicillin, oxacillin, and streptomycin. The molecular characterization revealed that 15 isolates harbored both hemolytic and non-hemolytic enterotoxin genes. Cotreatment of B. cereus spores-contaminated rice pudding with D-tryptophan at a concentration of 40 mM and L-ascorbic acid at a concentration of 3% revealed a significant reduction (P < 0.05) in the spore growth. Therefore, D-tryptophan and L-ascorbic acid are considered promising eco-friendly food preservatives with anti-B. cereus effects in the dairy industry.