The effect of the degree of crystallinity on the fracture toughness of titanium–PEKK interfaces was investigated experimentally. The level of crystallinity at the interface was varied by employing different processes commonly used in aerospace, namely autoclave consolidation, press-forming and annealing. The fracture toughness was assessed via the Double Cantilever Beam test, while the polymer degree of crystallinity was evaluated via Differential Scanning Calorimetry. Fracture surfaces were analyzed using confocal microscopy, SEM and AFM, to correlate the degree of crystallinity to the failure mechanisms and the toughness. The samples with a high degree of crystallinity exhibited a lower fracture toughness and a dominant cohesive failure, consisting of a combination of brittle fracture of the spherulites, and ductile fracture of the amorphous regions between the spherulites. Lowering the degree of crystallinity led to a higher fracture toughness, due to extensive plastic deformation of the amorphous polymer. In addition, fractography showed a transition from cohesive to interfacial failure in the case of a low degree of crystallinity. Our results show that the crystalline structure of the polymer has to be taken into account when optimizing the performance of metal–composite hybrid joints based on thermoplastic matrices.