Sulfur‐containing chiral heterocyclic secondary alcohols are relevant intermediates in the preparation of enantiomerically pure compounds endowed with biological activity. In this report, we evaluated the reductive potential of different lactic acid bacteria as whole‐cell biocatalysts of the enantioselective reduction of 1‐(thiophen‐2‐yl)ethanone (1). Enterococcus faecium BY48, isolated from boza, a cereal‐based fermented beverage, was found to be the best biocatalyst in our initial investigations. Using whole‐cell preparations of E. faecium BY48, we then systematically analyzed the reaction parameters (pH, incubation period, agitation speed, and temperature) to optimize the yield, the enantiomeric excess (e. e.), and the conversion leading to (S)‐1‐(thiophen‐2‐yl)ethanol [(S)‐2]. The target derivative, which is a precursor in the synthesis of biologically active chiral compounds, was obtained in enantiomerically pure form, gram‐scale amounts, and high yield. This is also the first report that the manufacture of (S)‐2 in excellent conversion, yield, enantiopure form, and gram scale used whole‐cell biocatalyst. This whole‐cell E. faecium BY48 biocatalyzed reaction is a clean, environmentally friendly, and cost‐effective process, representing a valuable alternative to chemical catalysis or previously reported biocatalytic procedures in the preparation of (S)‐2.