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An efficient method for the C3-glucuronidation of bile acids is developed under flow conditions. A modular mesoreactor assisted flow set-up was combined with statistical design of experiments to speed up the optimization of the Koenigs–Knorr reaction in terms of yield, regioselectivity, costs, as well as technical and practical standpoints. Using the optimal conditions, selective glucuronidation of naturally occurring bile acids was successfully achieved offering a new, valuable route to C3-glucuronidated bile acids useful for biological, diagnostic and PK/ADMET investigations.