A recently developed synchrotron-based imaging technique, X-ray diffraction microtomography (XRD-CT), has been applied here for the first time to a complex system, the hydrating Portland cement paste, in order to monitor the evolution of microstructure and phase formation with a 3D non-invasive imaging approach. The ettringite-XRD-peak-based image reconstructions, combined with transmission microtomography (X-microCT) images, allowed to assess the ubiquitous distribution of this phase, which appears early in the hydration process and showed its preferential concentration in the relatively less compact regions of the paste. The comparison of greyscale histograms for cement pastes after 9 and 58 h from hydration showed an increase of ettringite content with age, in agreement with the quantitative Rietveld analysis of the sum patterns. By renormalizing the greyscale histograms to the relative weight fraction, as obtained from Rietveld refinements, a new technique which allows estimation of phase contents with spatial resolution has been developed. The results achievable by combining XRD-CT, X-microCT and Rietveld appear very promising to provide experimental snapshots of the cement hydration process to be compared with results obtained from computer simulations.