Reactor automation is a transformative force for chemical processes, but the potential of reaction monitoring for machine-assisted autonomous biocatalytic reaction optimization is still largely unexplored. To address this gap, we report on automated reactor optimization for biocatalytic flowthrough microreactors. For this purpose, the inline NMR analysis of an enzymatically catalyzed stereoselective reduction of a prochiral diketone was combined with a self-developed opensource analysis and control software. The algorithm is continuously fed with spectra from a benchtop NMR instrument acquired from a reaction solution from a microreactor filled with biocatalytically active materials and adjusts the flow rate of the pumps to achieve predetermined target concentrations of the product. We show that through this automated coupling of data analysis and process parameterization, for example, maximum conversion efficiency can be achieved for a given bioreactor. This work illustrates the potential of inline NMR reaction monitoring for biocatalytic processes and provides a starting point for innovation to develop automated processes for precision biocatalysis through integrated data analysis.