PEEK-OPTIMA™ is being considered as an alternative to cobalt chrome (CoCr) in the femoral component of total knee replacements. To date, investigations of ultra-high molecular weight polyethylene (UHMWPE)-on-PEEK have shown an equivalent wear rate to conventional implant materials under standard conditions. In this study, the third body wear performance of UHMWPE-on-PEEK was directly compared to UHMWPE-on-CoCr in a series of pin-on-plate studies using two approaches for third body damage. Damage simulation with particles of bone cement showed a significant (p < 0.001), four-fold increase in the mean surface roughness of PEEK plates compared to CoCr. However, wear simulation against the damaged plates showed no significant difference in the wear of UHMWPE pins against the different materials (p = 0.59), and a polishing effect by the pin against the PEEK plates was observed. Scratching PEEK and CoCr counterfaces with a diamond stylus to create scratches representative of severe third body damage (4 µm lip height) resulted in a significantly higher (p = 0.01) wear of UHMWPE against CoCr compared to PEEK and again, against PEEK plates, polishing by the UHMWPE pin led to a reduction in scratch lip height. This study shows that in terms of its wear performance under third body wear/damage conditions, UHMWPE-on-PEEK differs from conventional knee replacement materials.