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Introduction: The use of medicinal plants to cure human diseases is going on since the development of human civilization. Also, the discovery of antibiotics had profound impact to reduced death rates against various pathogens but due to rise of resistance against these antibiotics are serious threats for human health. Henceforth, the world is looking for alternative approach and the use of active plant metabolites are one of them. Multidrug resistant Shiga toxin producing Escherichia coli (MDR STEC) are life threatening microorganisms worldwide and their ability to produce aggregated biofilm makes them tolerant to many antibiotics used for treating STEC infections. In this study effect of plant metabolites were studied against MDR STEC samples. Methods: The different parts of 10 medicinal plants reported from central India were used in this study. Extract preparation and active fractions were used to test antimicrobial activity against MDR-STEC through measuring zone of inhibition. The biofilm structure was observed using electron microscopy. Results: Total 20 MDR STECs were identified out of 100 STEC samples. The intimin (eae) gene responsible for drug resistance was present in 18 (90%) MDR STEC samples. STEC were producing more aggregated biofilm layer as compare to sensitive E. coli. The plant extracts isolated from Acacia auriculiformis, Albizia lebbeck and Gliricidia sepium showed significantly high antimicrobial activity against MDR STEC as compared to various antibiotics. Conclusions: The study will be helpful to develop new or alternate antimicrobial agents and therapy against MDR STEC by using metabolites from medicinal plants.