Purpose To determine the prevalence and virulence determinant genes of nasal colonization by Staphylococcus aureus among food handlers in Tripoli, Lebanon. Methodology Within a cross-sectional study design, nasal swab specimens were collected. Epidemiological and microbiological investigations were performed through conventional culture and MALDI-TOF-MS. Antibiotic susceptibility patterns and genetic virulence determinants including enterotoxin genes were also investigated for all isolates. Results The data herein show that S. aureus nasal carriage is highly prevalent (23.8 %), and that the rate of methicillin-resistant S. aureus (MRSA) carriage was twice as high as in our last report in 2008. Several enterotoxin genes were detected in five isolates including one MRSA and four methicillin-sensitive S. aureus . Conclusion To our knowledge, this is the first investigation in the last decade to examine the carriage prevalence of S. aureus among food handlers in Lebanon. This work reports a concerning level of MRSA, and enterotoxin-producing S. aureus nasal carriage, which could potentially act as a contamination reservoir and lead to food poisoning.