Kefir is a fermented milk containing microorganisms showing several properties beneficial to health. In the present work the safety aspects and beneficial properties of kefir-isolated Enterococcus strains were investigated for the first time. Enterococcus strains were identified as Enterococcus durans using phenotypical and molecular characterisation methods. Neither resistance to clinically important antibiotics, nor genes encoding for eight different virulence factors were found. Interestingly, selected E. durans strains were able to inhibit different Gram+ and Gram− pathogens. These strains were able to survive simulated gastrointestinal conditions and showed a similar power of adhesion to mucins. Of note, the E. durans strains possessed anti-inflammatory properties as demonstrated by a significant inhibition of flagellin-induced response on Caco-2 cells. Our results indicate that the presence of E. durans in kefir does not represent a threat to consumers' health, and shows their potential both functionality and as probiotics.