The microscale fracture modeling of concrete requires explicit descriptions of the microstructure and the fracture properties of its constituents. The identification of fracture properties of mortar was carried out by numerical analyses of two in situ (via X-ray tomography) mesoflexural tests on small-scale specimens. A realistic mesh was created for mechanical simulations to be run. The experimental kinematic fields were measured by processing the reconstructed volumes via Digital Volume Correlation. The measured displacements were used as kinematic boundary conditions to simulate three-point flexural tests. The full dataset consisting of realistic geometry and experimental boundary conditions, allowed for full simulations of the performed tests. A phase-field model for brittle materials was selected to describe damage of the cement paste, and debonding at the matrix-aggregate interfaces was modeled with a cohesive zone model. The fracture paths and ultimate forces simulated with the phase-field model were consistent with the experiment thanks to representative microstructure and boundary conditions. In both tests, the predicted crack path changed because of interface debonding. The introduction of cohesive interface elements did not significantly improve the faithfulness of the path prediction. This study demonstrates the potential of microscale simulations of in situ tests for model identification, validation and development at the microscale of mortar.