Contamination of meat with microorganisms during slaughter is inevitable. Hygiene management systems (HMSs) such as the Hygiene Assessment System (HAS) and Hazard Analysis Critical Control Point (HACCP) are used to prevent the contamination of beef with both spoilage and pathogenic microorganisms during slaughter. This study compared the effect of the HAS alone and a combination of HAS + HACCP on the microbiological quality of beef and investigated the survival of Escherichia coli O157:H7 co-cultured with different levels of Pseudomonas fluorescens and Lactobacillus plantarum on fresh beef. HAS alone and HAS combined with HACCP systems were each represented by two abattoirs. Sponge swab samples were collected from chilled beef carcasses for indicator organisms: Aerobic Plate Counts (APC), Enterobacteriaceae, Pseudomonas spp., and lactic acid bacteria. Swabs were also collected for pathogenic bacteria: E. coli O157:H7, Staphylococcus aureus and Salmonella spp. There was no significant difference between the microbiological quality of beef carcasses processed in the abattoirs with the HAS and that of beef carcasses processed in abattoirs with combined HAS + HACCP. E. coli O157:H7 was isolated from carcasses processed in an abattoir with the combined HAS + HACCP system. Moreover, although overall S. aureus counts at all abattoirs were comparable, a higher incidence (47% of carcasses) was obtained from an abattoir with combined HAS + HACCP. Salmonella spp. was not detected during the study. The microbiological quality of beef at HAS abattoirs is not significantly different to that of beef processed at HAS + HACCP abattoirs. The combined HAS + HACCP did not prevent contamination of beef carcasses with E. coli O157:H7 and S. aureus. Effective implementation of HAS can reduce contamination of beef with spoilage and pathogenic microorganisms. The effect of different levels of P. fluorescens (102 and 106 log10 cfu/ml) and L. plantarum (102 and 104 log10 cfu/ml) on the survival of E. coli O157:H7 on beef loins was investigated. Sterile beef loins inoculated with E. coli O157:H7 and P. fluorescens were aerobically stored for 7 days at 4°C, while those inoculated with E. coli O157:H7 and L. plantarum were vacuum-packaged and stored for 8 weeks at 4°C. APC, E. coli O157:H7 and either P. fluorescens or L. plantarum counts were determined at different storage intervals. For the aerobically packaged beef loins, E. coli O157:H7 was detected throughout the 7-day storage period regardless of the P. fluorescens level in the inoculum. For the vacuum packaged beef loins, similar inoculum levels of E. coli O157:H7 and L. plantarum allowed E. coli O157:H7 to survive until week 5 of storage, while a higher inoculum level of L. plantarum inhibited E. coli O157:H7 from week 3. Once fresh beef has been contaminated with E. coli O157:H7 the level of P. fluorescens in the background flora does not inhibit its survival and growth. However, under vacuum storage, the application of L. plantarum as a biopreservative inhibits the survival of E. coli O157:H7 on beef. Comprehensive strengthening of preventive strategies is required to eliminate contamination of beef carcasses with E. coli O157:H7. Bacterial contamination of carcasses during slaughter is inevitable. Effective implementation of HAS at abattoirs produces beef carcasses of microbiological quality comparable to that produced through the use of combined HAS and HACCP. While the level of P. fluorescens on beef does not inhibit the survival of E. coli O157:H7 on aerobically stored beef, the combination of L. plantarum, and low storage temperature inhibits the survival of this pathogen on beef under vacuum storage.