Outbreaks related to foodborne diseases are a major concern among health authorities, food industries, and the general public. Escherichia coli (E. coli) is a pathogen associated with causing multiple outbreaks in the last decades linked to several ready to eat products such as meat, fish, dairy products, and vegetables. The ingestion of contaminated food with pathogenic E. coli can cause watery diarrhea, vomiting, and persistent diarrhea as well as more severe effects such as hemorrhagic colitis, end-stage renal disease, and, in some circumstances, hemolytic uremic syndrome. Essential oils (EOs) are natural compounds with broad-spectrum activity against spoilage and pathogenic microorganisms and are also generally recognized as safe (GRAS). Particularly for E. coli, several recent studies have been conducted to study and characterize the effect to inhibit the synthesis of toxins and the proliferation in food systems. Moreover, the strategy used to apply the EO in food plays a crucial role to prevent the development of E. coli. This review encompasses recent studies regarding the protection against pathogenic E. coli by the use of EO with a major focus on inhibition of toxins and proliferation in food systems.