This paper presents the outcome of a study focused on the evolution of internal damage in fresh cement mortar over 25 hours of hardening. In situ timelapse X-ray computed micro-tomography (μXCT) imaging method was used to detect internal damage and capture its evolution in cement mortar hardening. During μXCT scans, the temperature released during the cement hydration was measured, which provided insight into the internal damage evolution with a link to a hydration temperature rise. The measured temperature during cement mortar hardening was compared with an analytical model, which showed a relatively good agreement with the experimental data. Using 20 CT scans acquired throughout the observed cement mortar hardening, it was possible to obtain a quantified characterisation of the porous space. Additionally, the use of timelapse μXCT imaging over 25 hours allowed for studying the crack growth inside the meso-structure including its volume and surface characterisation. The results provide valuable insights into cement mortar shrinkage and serve as a proof-of-concept methodology for future material characterisation.