The fracture process in self-healing concrete with embedded brittle capsules entails challenges in terms of understanding how and when these capsules break to release the agent. This paper presents a combined experimental–numerical investigation in which a versatile three-dimensional simulation model is developed to investigate the fracture of this type of beams under three-point bending load. The model allows for correlating the overall strength with different damage events occurring in every constituent: the concrete, the capsules and the capsule-concrete interface. The constitutive concrete damage model uses a pressure-dependent failure initiation criterion followed by a bilinear softening law, whose parameters are validated by using a modified Nelder-Mead optimization algorithm enriched with user-defined constraints aimed at increasing the convergence ratio. The validated virtual model demonstrates that the ratio of capsule slenderness to concrete-capsule interface strength is the key parameter for an effective self-healing process as it gives full control to break the capsule at the right moment. The shorter the capsule is, the longer the breakage process can be. Additionally, it has been found that by increasing the length of the capsules can help to enhance the overall fracture energy of the beam even after fully broken.