Biphasic biocatalytic reactions have gained much attention in the field of enzyme-catalysed synthesis. As most components being of relevance for the pharmaceutical industry are hydrophobic, often biphasic reaction media turned out to be the solvent system of choice. However, in spite of successful reaction courses practical difficulties in the downstream-processing, in particular extremely difficult phase separations due to emulsification and precipitation, represent a challenge to overcome in process development. In this work, we report our studies on the benefits of a simple flow set-up being capable to minimise such work-up limitations. In detail, a segmented flow system based on a biphasic MTBE/buffer mixture was successfully applied for two types of enzymatic reductions of a hydrophobic ketone in the presence of an alcohol dehydrogenase (ADH) as an enzyme class being known for their excellent enantioselectivity and successful utilization in the synthesis of a range of active pharmaceutical ingredients. The applicability of this flow system was demonstrated with two different enzymes as well as different substrates. Besides an ADH from Lactobacillus brevis, an ADH from Ogatea minuta was utilized for the reduction of acetophenone and 2,2,2-trifluoroacetophenone, respectively.