Polyetheretherketone (PEEK) is widely employed in orthopedic applications due to its bone-mimetic mechanical properties and excellent biocompatibility, establishing it as a promising candidate for bone repair and regeneration. However, the investigation of structural integrity and microstructural features of PEEK implants has remained limited owing to its low atomic number (Z < 8) and hierarchical microstructure. This study presents a comparative characterization of PEEK implants by integrating laboratory X-ray computed tomography (CT) and synchrotron X-ray phase-contrast tomography (SXCT). Laboratory X-ray CT, operating on absorption contrast mechanisms, demonstrates adequate capacity for visualizing macroscopic defects and pore architectures, but exhibits limitations in resolving subtle density variations. In contrast, SXCT, employing phase-contrast imaging, significantly enhances discrimination of ultra-low-contrast features, including interconnected pore networks and localized density gradients. This work elucidates the complementary advantages and inherent limitations of both the imaging modalities for characterizing PEEK-based biomaterials. Furthermore, it demonstrates the potential extensibility of this comparative approach to other polymer composites, offering a methodology to investigate material–tissue interactions in orthopedic research and advancing the development of next-generation implantable devices.