Inorganic germicides, such as chlorine and its derivatives, are widely used against surface pathogens in various food industries. Due to the potential toxicity of the disinfectants and their by-products, alternative and dosage-efficient methods should be developed to secure food safety and hygiene. Here, we present a natural organic acid-based combinatorial treatment that efficiently inactivated the selected foodborne pathogenic bacterial strains even at low concentration. The individual and/or combinatorial treatments of citric (CA), malic (MA), and phytic acid (PA) inactivated Escherichia coli and Staphylococcus aureus in concentration- and time-dependent fashion. At one selected concentration, the mixture of acids (CA+MA+PA) efficiently reduced E. coli and S. aureus viability by approximately 99.9% within 10 min. The combined application of three organic acids resulted in higher germicidal activity than the sum of the individual treatment inactivation levels, suggesting a synergistic effect among the acids. Our combined acid treatment disrupted bacterial membrane integrity and increased the intracellular reactive oxygen species. The inactivation efficiency of the presented organic acid mixture was also verified for Salmonella Typhimurium, Pseudomonas aeruginosa, and Listeria monocytogenes. In conclusion, we established a composition of natural acid-based mixture, allowing efficient surface disinfection against various Gram-positive and negative pathogenic bacteria through a synergistic effect mechanism.