The growing intention to replace chemical food preservatives with plant-based antimicrobials that pose lower risks to human health has produced numerous studies describing the bactericidal properties of biopreservatives such as essential oils (EOs) in a variety of products, including cheese. This study aimed to perform a meta-analysis of literature data that could summarize the inactivation of Escherichia coli in cheese achieved by added EOs; and compare its inhibitory effectiveness by application method, antimicrobial concentration, and specific antimicrobials. After a systematic review, 362 observations on log reduction data and study characteristics were extracted from 16 studies. The meta-regression model suggested that pathogenic E. coli is more resistant to EO action than the non-pathogenic type (p < 0.0001), although in both cases the higher the EO dose, the greater the mean log reduction achieved (p < 0.0001). It also showed that, among the factual application methods, EOs’ incorporation in films render a steadier inactivation (p < 0.0001) than when directly applied to milk or smeared on cheese surface. Lemon balm, sage, shallot, and anise EOs showed the best inhibitory outcomes against the pathogen. The model also revealed the inadequacy of inoculating antimicrobials in cheese purposely grated for performing challenge studies, as this non-realistic application overestimates (p < 0.0001) the inhibitory effects of EOs.