Enzyme catalysis in two-phase systems, particularly in the functionalization of siloxanes, is a new challenge for biocatalysis. On the basis of three different reaction systems, stirred tank reactor, enzyme membrane reactor and micro mixer, the influence of the phase boundary layer along the interface between an aqueous system and an organosiloxane on the synthesis of hydroxyalkylfunctionalized siloxanes is discussed and solutions presented. Micro mixers produce, through a large surface area to volume ratio, boundary layers within which through a formate dehydrogenasecatalyzed reaction the conversion of 1,3-bis-(3-formoxypropyl)tetramethyldisiloxane to 1,3-bis-(3-hydroxypropyl)tetramethyldisiloxane can be achieved. In contrast, in a stirred tank reactor even after 96 h only 45 % of the formoxy siloxane has been converted.