<p>Probiotics have gained increasing attention due to their potential health benefits, antimicrobial properties, and role in promoting overall well-being. In this context, the identification of novel bacterial strains with relevant functional properties and high stability under food processing conditions is essential. This study aimed to identify an isolate from Brazilian semi-hard cheese and assess the presence of virulence genes and genes involved in biogenic amine production, as well as to evaluate bacteriocin production and the in vitro probiotic potential of the strain. Additionally, the strain was microencapsulated by spray-drying to enhance its resistance under gastrointestinal and storage conditions. The isolate was identified as <i>Enterococcus faecium</i> EM03 through 16&#xa0;S rDNA gene sequencing. In vitro safety testing showed susceptibility to most antibiotics tested, with resistance only to ciprofloxacin and gentamicin. Molecular analyses confirmed the absence of genes associated with biogenic amine synthesis and key virulence factors typically considered in Enterococcus safety assessments (<i>ace</i>, <i>asa</i>1, <i>cyl</i>A, <i>ef</i>aA, <i>esp</i>, and <i>gel</i>E). Conversely, genes associated with bacteriocin production (<i>ent</i>B, <i>ent</i>P, L50AB, <i>Ian</i>M, and <i>Ian</i>C) were detected, supporting the results showing inhibition of <i>Listeria monocytogenes</i> and <i>E. faecalis</i> by proteinaceous compounds. Additionally, the strain showed high resistance under simulated gastrointestinal conditions, and microencapsulation by spray-drying further enhanced its stability, allowing probiotic survival for up to 60 days and maintaining good resistance to simulated gastrointestinal conditions while keeping the microparticle properties consistent. Overall, <i>E. feacium</i> EM03 showed strong probiotic potential, combining safety, antimicrobial properties, and technological stability, supporting its use in the development of functional foods.</p>