A new isolate, Rhodotorula sp. AS2.2241, capable of reducing acetophenone and α-bromoacetophenone with high stereoselectivity, was further studied to exploit its potential in the asymmetric reduction of silicon-containing ketones to silyl alcohols. After encapsulation, the cells were used in an aqueous or an aqueous/organic solvent biphasic system for the asymmetric reduction of acetyltrimethylsilane (ATMS) to prepare (−)-1-trimethylsilylethanol [(−)-TMSE]. It has been found that higher product yield and product enantiomeric excess could be achieved with immobilized cells in an aqueous/organic solvent biphasic system. For optimization of the reaction, various influential variables, such as the volume ratio of the aqueous phase to the organic phase, the hydrophobicity of the organic solvent, reaction temperature, buffer pH of the aqueous phase and the shaking speed, were examined with respect to the initial reaction rate, the product yield and the enantiomeric excess (e.e.) of TMSE formed. All the factors mentioned above had influences on the reaction to some extent. Isooctane was found to be the most suitable organic phase for the reaction. The optimum volume ratio of the aqueous phase to the organic phase, reaction temperature, buffer pH and shaking speed were 1/1, 40 °C, 6.5 and 150 rpm, respectively under which the product yield and the product enantiomeric excess were as high as 99 and 90%, which are much higher than those previously obtained by enantioselective reduction of acylsilanes.