Background. The mechanical response and damage mechanisms of heterogeneous cementitious materials result from the mechanical properties of their constituents at the mesoscale. Objective. In this study, a finite element based Digital Volume Correlation (FE-DVC) method with mechanical regularization tailored for heterogeneous materials was applied to study crack propagation in mortar. Method. A realistic 3D mesh was built consistently with the actual microstructure based on high resolution X-ray tomography. A notched mesobeam was subjected to in situ three-point flexure. Results. The introduction of mechanical contrast in DVC analyses allowed the strain heterogeneities related to the underlying microstructure to be described and inelastic strain localization due to cracks to be captured. Furthermore, the relaxation of mechanical regularization in damaged elements improved the trustworthiness of displacement measurements. Conclusion. Estimations of crack opening displacements and characterization of the crack morphology were carried out, providing insights into the damage processes at the mesoscale.