Pathogenic micro-organisms from contaminated food are capable of causing serious infections and hence this issue has become a healthcare problem globally. The contamination may occur, either directly by an infected food handler, or indirectly through contact with a food contact surface that has been previously contaminated by an infected food handler. The current study was aimed to detect the pathogenic bacteria from food handlers in Ha’il region of Saudi Arabia. In this study, 152 bacterial isolates were collected from 50 food handlers. Identification of bacterial isolates was performed by conventional methods as well as by automated methods using Microscan, VITEK 2 and MALDI-TOF-MS. The results of conventional methods showed, 28.3% (43/152) bacterial isolates were Gram-positive and 71.7% (109/152) were Gram-negative. Among the Gram-positive isolates, E. faecalis, S. aureus and E. faecium were found to be 8.5% (13/152), 7.2% (11/152) and 4% (6/152) respectively. Among Gram-negative isolates, P. mirabilis, E. coli, E. cloacae and K. pneumoniae were found to be 12.5% (19/152), 11% (17/152), 11% (17/152) and 10.5% (16/152) respectively. The antibiotic susceptibility of the bacterial isolates in our study showed that 100% S. aureus were ciprofloxacin resistant. Additionally, 62% E. faecalis were resistant to gentamicin, 19% E. coli and 12% K. pneumoniae were found to be ESBL positive. The identification of bacterial isolates by 3 automated methods, showed that 93% (141/152), 94% (143/152) and 96% (146/152) bacterial isolates were correctly identified by Microscan, VITEK 2 and MALDI-TOF-MS respectively. Thus MALD-TOF-MS proves to be the economical, fast and accurate method for identification of food borne pathogens. Incorporating this technique into food microbiology would lead to more successful and rapid identification of pathogenic bacteria from food sources.