The structure and performance of polyurethane (PU) foams are strongly driven by the stoichiometry of the polyaddition reaction, quantitatively described by the isocyanate index. It determines the balance between isocyanate and hydroxyl groups in the reacting system and is affected by the introduction of additional functionalities originated, e.g., from applied fillers. Nevertheless, this issue is hardly taken into account in research works. Herein, the structure and performance of PU/ground tire rubber (GTR) composites differing in their isocyanate index (from 0.8 to 1.2) and prepared with and without considering the GTR functionalities in formulation development were investigated. Incorporating GTR into the PU matrix led to a reduction in average cell diameter (from 2 to 30% depending on the isocyanate index) compared to unfilled foams. However, formulation adjustments did not show a significant impact on cellular structure. The only decrease in open cell content was noted, from 10% for the 0.9 index to 40% for 1.2. Such changes were related to the increasing strength of the PU cellular structure able to maintain inside the increasing amount of carbon dioxide. On the other hand, considering hydroxyl values of GTR noticeably affected the thermomechanical performance of composites. The shift of glass transition temperature (Tg), even by 10 °C for 1.2 isocyanate index, enhanced the performance of materials, which was expressed in an 8-62% drop in the composite performance factor, pointing to the enhanced reinforcing effect resulting from filler incorporation. The stiffening of foams, related to the variations in PU segmental structure, also caused minor changes in the course of thermal degradation of PU/GTR composites due to the inferior thermal stability of hard segments. The obtained results provide important insights into the development of formulations of PU composites filled with materials containing reactive functional groups able to disrupt the stoichiometric balance of the polyaddition reaction.