The probiotic features of a new Enterococcus faecium strain isolated from camel rumen were investigated. The isolate identified as E. faecium 96B4 exhibited notable tolerance to gastrointestinal conditions, with high cell viability at pH 1.5 after 3 h (about 7.48 log10 cfu mL−1). Besides complete inhibition of Listeria monocytogenes growth, E. faecium 96B4 showed high hydrophobicity, auto- and co-aggregations abilities. It showed 76.33% cholesterol assimilation ability and boosted the extracellular unsaturated fatty acid content up to 25.53% in the presence of soybean oil as a substrate. Moreover, 96.17 ± 3.52 μg mL−1 conjugated linoleic acid production and 2.56 fold increase in oleic acid content were highlighted. Significant diacetyl production ability was also demonstrated. E. faecium 96B4 passed the safety assessment successfully. The association between the microbiome and host health makes the camel, as a unique animal, a rich source of beneficial microorganism candidates for designing future foods.