School canteens are critical environments for student health, yet they frequently act as reservoirs for multidrug-resistant foodborne pathogens. This study aimed to evaluate the microbiological quality of environmental surfaces and the hands of food handlers in Al-Marj City, Libya, while determining the antimicrobial susceptibility of the isolates. During the 2024-2025 academic year, 60 swabs were collected from 15 school canteens. Bacteriological identification was conducted using selective media and comprehensive biochemical assays. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disc diffusion method. The overall contamination rate was 53.3%. Escherichia coli was the most prevalent isolate (43.8%), followed by Staphylococcus aureus (34.4%) and Proteus mirabilis (21.9%). A statistically significant disparity was observed in hygiene outcomes based on management gender: male-managed facilities exhibited a 59.6% contamination rate, whereas female-managed facilities showed 12.5%. The high prevalence of fecal indicators and opportunistic pathogens necessitates urgent regulatory oversight and the implementation of mandatory food safety certification for canteen personnel.