Lactic acid bacteria (LAB) isolated from soy milk were used to produce a multifunctional fermented food. Seven isolates were screened for their ability to produce peptides and free isoflavones in soy milk. The antihypertensive, antioxidant, and anti-inflammatory properties of the resulting fermented soy milks were evaluated in vitro using biochemical assays. Isolates 1-5 were found to be producers of fermented soy milk with angiotensin I converting enzyme inhibitory activity (ACEI). Isolate 3 was found to be a producer of free isoflavones that increased the antioxidant and anti-inflammatory potential of fermented soy milk. LAB isolates 2-5 were submitted to genetic profiling and a characterization scheme. These isolates were identified as Enterococcus faecium , and none of them contained virulence determinants or resistance to antibiotics. In conclusion, this study shows that the application of E. faecium isolate 3 for multifunctional food production from soy milk could be a promising strategy in the prevention therapy against cardiovascular disease.