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Enterococcus faecium is a promising probiotic with potential antimicrobial effects. This study aimed to evaluate the probiotic and antimicrobial properties of E. faecium MBBL3, isolated from healthy cow milk, against bovine mastitis pathogens Klebsiella pneumoniae MBBL2 (Kp MBBL2) and Escherichia coli MBBL4 (Ec MBBL4), using comprehensive genomic and functional analyses. The genome assembly and functional annotations of MBBL3 unveiled many important probiotic traits, and comparative genomic analysis demonstrated its high degree of genetic similarity with other Enterococcus strains. MBBL3 exhibited the ability to ferment a diverse range of carbohydrates and possessed 76 genes linked to carbohydrate-active enzyme, including five key CAZy families with potential antimicrobial activity. Additionally, MBBL3 harbored genes essential for bile salt and acid tolerance, stress resistance, and surface adhesion. Furthermore, MBBL3 was found to harbor gene clusters encoding secondary metabolites with antimicrobial potentials. Safety evaluations revealed a low pathogenic potential, while in-vitro assays demonstrated antibiotic susceptibility and a reduction in the growth of Kp MBBL2 and Ec MBBL4, respectively. It's bacteriocin Enterolysin_A exhibited strong molecular interactions with virulence-associated proteins of the mastitis pathogens. Thus, the promising probiotic potential and antimicrobial activity of E. faecium MBBL3, particularly against mastitis-related pathogens coupled with its safety profile, render it a promising candidate for further investigation.