Analysis of catalytic organic transformations in flow reactors and detection of short-lived intermediates are essential for optimization of these complex reactions. In this study, spectral mapping of a multistep catalytic reaction in a flow microreactor was performed with a spatial resolution of 15 mu m, employing micrometer-sized synchrotron-based IR and X-ray beams. Two nanometer sized Au nanoclusters were supported on mesoporous SiO2, packed in a flow microreactor, and activated toward the cascade reaction of pyran formation. High catalytic conversion and tunable products selectivity were achieved under continuous flow conditions. In situ synchrotron-sourced IR microspectroscopy detected the evolution of the reactant, vinyl ether, into the primary product, allenic aldehyde, which then catalytically transformed into acetal, the secondary product. By tuning the residence time of the reactants in a flow microreactor a detailed analysis of the reaction kinetics was performed. An in situ micrometer X-ray absorption spectroscopy scan along the flow reactor correlated locally enhanced catalytic conversion, as detected by IR microspectroscopy, to areas with high concentration of Au(III), the catalytically active species. These results demonstrate the fundamental understanding of the mechanism of catalytic reactions which can be achieved by the detailed mapping of organic transformations in flow reactors