Rapid cooling in fast-rate manufacturing processes such as additive manufacturing and stamp forming limits the development of crystallinity in semicrystalline polymer nanocomposites and, therefore, potential improvements in the mechanical performance. While the nucleation, chain mobility, and crystallization time from rapid cooling are known competing mechanisms in crystallization, herein we elucidate that the crystalline morphology and architecture also play a key role in tuning the mechanical performance. We explore how modifying the spherulite morphology via a cellulose nanocrystal (CNC) and graphene nanoplatelet (GNP) hybrid system in their pristine form can improve or preserve the mechanical properties of poly(ether ether ketone) (PEEK) nanocomposites under two extreme cooling rates (fast -460 °C/min and slow -0.7 °C/min). A scalable manufacturing methodology using water as the medium to disperse the powder system was developed, employing a CNC as a dispersing agent and stabilizer for PEEK and GNP. Despite the expected limited mechanical reinforcement due to thermal degradation, CNCs significantly impacted PEEK's crystalline architecture and mechanical performance, suggesting that surface interactions via lattice matching with PEEK's (200) crystallographic plane play a critical role in engineering the microstructure. In fast cooling, the CNC and CNC:GNP systems reduced the crystallinity, respectively, yet led to minimizing the reduction in the tensile strength and maintaining the tensile modulus at the Neat level in slow cooling. With slow cooling, crystallinity remained relatively unchanged; however, the addition of CNC:GNP improved the strength and modulus by ∼10% and ∼16%, respectively. These findings demonstrate that a hybrid nanomaterial system can tailor PEEK's crystalline microstructure, thus presenting a promising approach for enhancing the mechanical properties of PEEK nanocomposites in fast-rate processes.