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Poly(etheretherketone) (PEEK) implants suffer from poor osseointegration because of chronic inflammation. In this study, we hypothesized that adding NH and COOH groups to the surface of PEEK could modulate macrophage responses by altering protein adsorption and improve its osseointegration. NH and COOH-functionalized PEEK surfaces induced pro- and anti-inflammatory macrophage responses, respectively, and differences in protein adsorption patterns on these surfaces were related to the varied inflammatory responses. The macrophage responses to NH surfaces significantly reduced the osteogenic differentiation of mesenchymal stem cells (MSCs). MSCs cultured on NH surfaces differentiated less than those on COOH surfaces even though NH surfaces promoted the most mineralization in simulated body fluid solutions. After 14 days in rat tibia unicortical defects, the bone around NH surfaces had thinner trabeculae and higher specific bone surface than the bone around unmodified implants; surprisingly, the NH implants significantly increased bone-binding over the unmodified implants, while COOH implants only showed a trend for increasing bone-binding. Taken together, these results suggest that both mineral-binding and immune responses play a role in osseointegration, and PEEK implant integration may be improved with mixtures of these two functional groups to harness the ability to reduce inflammation and bind bone strongly.