The present work describes some new improvements concerning the analysis of cement hydration processes using ‘pencil-beam’ synchrotron X-ray diffraction tomography. (i) A new filtering procedure, applied to the diffraction images, has been developed to separate the powder-like contribution from that of the grains in the diffraction images. (ii) In addition to improving the quality of the diffraction images for the subsequent analysis and tomographic reconstruction, the filtering procedure can also be used to perform a qualitative analysis of the crystallite size distribution, whenever the more standard approaches cannot be applied. (iii) Given the importance of the calcium silicate hydrate phase (C–S– H) in cements, a procedure to obtain its spatial distribution using the diffraction signal has been successfully applied, even though C–S–H is a highly disordered phase, almost amorphous to X-ray diffraction. (iv) The main result of this study has been to show that, in spite of the long measurement times required, it is possible to use in situ experiments at different aging times of cement pastes to monitor the cement evolution. This allowed the evolution of the microstructure during the acceleration and deceleration periods of the hydration process to be checked with unprecedented detail, since the quantitative spatial distribution of each phase (including C–S–H) dissolved or precipitated in the sample has been obtained. The reported approach opens up a range of opportunities for the investigation of complex multiphase systems and processes, including hydration and microstructural development in cements.