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Methodologies are developed for analyzing failure initiation and crack propagation in highly heterogeneous concrete mesostructures. Efficient algorithms are proposed in Python to generate and pack geometric features into a continuous phase. The continuous phase represents the mortar matrix, while the aggregates and voids of different sizes represent the geometric features randomly distributed within the matrix. The cohesive zone model (CZM) is utilized to investigate failure initiation and crack propagation in mesoscale concrete specimens. Two-dimensional zero-thickness cohesive interface elements (CIEs) are generated at different phases of the concrete mesostructure: within the mortar matrix, aggregates, and at the interfacial transition zone (ITZ). Different traction–separation laws (TSL) are assigned to different phases to simulate potential crack paths in different regions of the mesoscale concrete specimen. The mesoscale finite element simulations are verified using experimental results from the literature, with a focus on implementing mixed-mode fracture and calibrating its corresponding parameters with respect to the experimental data. In addition, the current study addresses the limited exploration of void effects in mesoscale concrete simulations. By investigating voids of diverse sizes and volume fractions, this research sheds light on their influence on the mechanical behavior of concrete materials. The algorithms for generating cohesive interface elements and concrete microstructures are described in detail and can be easily extended to more complex states. This methodology provides an effective tool for the mesostructural optimization of concrete materials, considering specific strength and toughness requirements.