The study was conducted to determine the incidence of E. coli serotypes in beef and chicken shawarma sandwiches, particularly E. coli O157:H7. The antibacterial activity of nano-emulsions (NEs) was evaluated, such as cinnamon and rosemary, against E. coli O157:H7. A total of 100 samples from ready-to-eat beef and chicken meat shawarma sandwiches (50 each) were isolated and identified as E. coli using a Sorbitol MacConkey (SMAC) agar assay. The results were confirmed by serology and polymerase chain reaction PCR using the phoA gene, which is specific for E. coli and the fliCH7 gene, which is specific for E. coli O157:H7. Cinnamon and rosemary NEs were prepared, characterized, and evaluated in vitro to determine the minimum inhibitory concentration (MIC) using a well diffusion method. The incidence of E. coli species isolated from beef and chicken shawarma sandwiches samples was 58% and 10%, respectively. While, E. coli O157:H7 was detected in 6% of beef shawarma sandwiches only. Both cinnamon and rosemary NEs exhibited antimicrobial activity against E. coli O157:H7, and the cinnamon NE was more effective compared with that of rosemary with a mean inhibition zone of 7.67 ± 1.202 mm and 7 ± 0.5774 mm at MIC 0.78% and 3.125%. Further studies are required to detect the safety of effectiveness of natural NEs in the food industry.