An efficient approach for high-quality X-ray absorption spectroscopy (XAS) measurements is proposed and exemplified by monitoring the nucleation of palladium nanoparticles from Pd(II) acetate. The idea of an X-ray beam passing through a microfluidic channel allowed for a significant improvement of the data quality to monitor in situ the early stages of palladium nanoparticle formation. The time evolution of Pd(II) and Pd(0) fractions was followed by collecting the spectra in seven subsequent channels and quantified by linear combination analysis of Pd foil and Pd acetate reference spectra. This work illustrates the application of XAS in microfluidics for chemical systems and might be used for obtaining structural information under reaction conditions in the presence of 4d metals.