BACKGROUND Animal manure frequently harbors pathogenic microorganisms such as Salmonella spp. and diarrheagenic Escherichia coli. A defined microbial consortium such as effective microorganisms (EM) can potentially be used as a biocontrol against manure‐borne human pathogens such as Salmonella and pathogenic E. coli. The objective of the study was to investigate the efficacy of EM to decontaminate cattle manure. RESULTS EM was first characterized by enumeration and identification of lactic acid bacteria (LAB), yeasts, actinomycetes and phototrophic bacteria (PB). The population density of LAB, yeasts, actinomycetes and presumptive PB was 6.9, 5.2, 5.9 and 3.9 log CFU g−1 respectively. LAB and yeast isolates were molecularly confirmed as Lactobacillus plantarum and L. casei (LAB) and Yarrowia lipolytica, Rhodotorula mucilaginosa and Picha manshurica (yeasts) respectively. Culture‐independent molecular analysis revealed the presence of additional species including L. parabuchneri and Enterococcus faecium (LAB) and bacterial spore‐formers Bacillus cereus and Clostridium spp. Application of EM to fresh cattle manure, inoculated with ~5–6 log CFU g−1 of antibiotic‐resistant strain of indicator organism E. coli ATCC 25922, resulted in complete elimination of the organism in 20 days, while survivors were still detected in the untreated counterpart. CONCLUSION EM can potentially be used for sustainable pathogen control in cattle manure for enhanced food safety and environmental health. © 2020 Society of Chemical Industry