Recently, due to their extraordinary strength-to-weight ratio and multi-functional applications, three-dimensional woven fiberglass sandwich structures have become a well-received topic by researchers and manufacturers. Nevertheless, using light and foam absorber materials as injected fillers within sandwich cores can improve their overall mechanical performance and, in particular, their fracture toughness behavior. This study evaluates the fracture toughness of three-dimensional woven fiberglass sandwich panels filled with natural nano-structured zeolite/polyurethane foams injected between their parallel panels. The Single-Edge Notched Bend test was carried out to understand the effect of the injected foam on the mode-I fracture toughness response. It is demonstrated that the polyurethane foam reinforced with natural nano-structured zeolite particles highly improved the fracture toughness of sandwich core panels. It was found that the presence of vertical glass yarns within the sandwich panel gallery resulted in a significantly higher toughness compared with typical sandwich panels of no reinforcing vertical columns confirmed by the crack propagation and observed failure mode. The SEM and EDX analyses were used to better understand the correlations amongst the specimen morphology, the cracks behavior, and the toughness exhibited by the fabricated specimens.