Currently, chlorine is the most widely used decontaminant in the minimally processed (MP) food industry. However, it does not achieve more than a 1–2 log reduction in bacterial populations. Efficient decontamination of MP produce could create a less competitive environment in which pathogens can multiply without restriction. Therefore, our objective was to test the efficacy of the biopreservative bacterial strain CPA-6 isolated from MP apples to control a non-pathogenic strain of Escherichia coli O157:H7, Salmonella and Listeria innocua on MP apples and peaches. Apple and peach plugs were co-inoculated with a suspension containing one of the pathogens (105 colony forming units (cfu) plug−1) and CPA-6 (106 cfu plug−1) and incubated at 20 °C or 5 °C. CPA-6 effectively inhibited the growth of, or reduced, in some cases to below the limit of detection, pathogen populations on both fruit incubated for 2 days at 20 °C and of E. coli on both fruit incubated at 5 °C, compared with the pathogen inoculated alone. The minimum effective dose required to inhibit any of the pathogens tested was 106 cfu plug−1 on both fruit and at both temperatures and it did not cause a hypersensitive reaction on tobacco plants. Finally, CPA-6 could not be assigned to any of the recognised species within the family Enterobacteriaceae based on phenotypic and 16S rRNA results. Therefore, this strain may be a suitable microorganism to use as a biopreservative culture to control the growth of food borne pathogens on MP fruit.