This work combines non-destructive X-ray micro-computed tomography (µCT) and scanning electron microscopy (SEM) to study the self-healing triggering mechanism in a system consisting of an epoxy resin, based on diglycidyl ether of bisphenol A, with embedded poly(urea-formaldehyde) (PUF) microcapsules filled with an amino-functional polysiloxane (PDMS-a) as a healing agent. µCT and SEM analyses proved that PDMS-a was effective in filling the microcrack areas, providing an efficient self-healing process, and confirmed that the main mechanisms for increasing fracture toughness are due to crack bowing and deflections. It was also observed that the diameter and shell thickness of the microcapsules are essential factors for their dispersion and integrity into the polymer matrix. PUF microcapsules with shell thickness of ca. 0.4 µm and diameters <60 µm were stable and well dispersed within the matrix. These findings shed light for understanding the increase of the fracture toughness, after self-healing, reported in our previous study of this system.