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A 2-step flow-based chemo-enzymatic synthesis of selected cinnamoyl tryptamines as potential cosmetic ingredients has been developed. A first reaction catalyzed by immobilized Pd(OAc)2 gave the acyl donors employed as starting material in the second step, with very good yields (67–70%) and rapid reaction times (30 min). A second bioreactor made of imm-MsAcT, a glyoxyl-agarose immobilized acyl transferase from Mycobacterium smegmatis, was employed for the fast and efficient preparation of the desired amides (58–70% m.c., 15 min). In-line work-up allowing for the recovery and reuse of the unreacted substrates was added downstream the process, enhancing its automation. The combination of flow facilities, high substrate-to-catalyst ratio and closed-loop strategies make this methodology a sustainable and cost-effective procedure. Computational studies were carried out to provide insights into the enzymatic active site and substrate recognition.