C−C bond forming enzymes, such as 2‐deoxyribose‐5‐phosphate aldolase (DERA), are an important class of enzymes in synthesis. The use of DERA, with its reaction routes to the double aldol product, is an established method for producing statin side chains in industry. Herein, the selective synthesis of 3‐hydroxyaldehydes as single aldol products of DERA is presented. Successful covalent immobilization of a suitable Escherichia coli (Ec) DERA variants with C47M and C47V exchanges, respectively, enabled their use in continuous synthesis. Precise reaction control using flow chemistry made the selective formation of 3‐hydroxyoctanal from hexanal possible. For optimization, a systematic approach of design of experiment (DoE) was used, resulting in 90 % conversion. Furthermore, five two‐step reaction systems have been established to scavenge the reactive single aldol product combining biocatalysis in flow mode and a consecutive chemical reactions step either in flow (continuous flow mode) or in batch (semi‐continuous flow mode).