In this study, the essential oils of the basal leaves (blEOs) and peduncles (pEOs) -stalks bearing flowers- of Scrophularia catariifolia were separately analyzed using GC-MS for the first time. The main components of two distinctive parts were determined as 4-hexen-1-ol (8.03/6.34%), 1-hexanol (5.48/9.15%), 3-octenol (16.94/6.83%), benzene ethanol (17.21/9.82%), and phytol (15.18/28.68%) for basal leaves and peduncles, respectively. The essential oils showed remarkable antimicrobial activity against the four food-borne pathogens tested. Pseudomonas aeruginosa, Clostridium perfringens, and Bacillus cereus were found to be more susceptible to peduncle essential oil. Two essential oils showed similar activity against Staphylococcus aureus. The essential oils were found to be inactive against Escherichia coli. These findings highlight the potential of S. catariifolia essential oils as natural antimicrobial agents for food safety and preservation. Further investigations are needed for their key applications.