Polyetheretherketone (PEEK) is a high-performance polymer with advantages over metallic biomaterials for application in spinal implants. In this study, hydroxyapatite (HA) coatings were deposited onto PEEK substrates using radio-frequency magnetron sputtering for the purpose of improving bioactivity. An intermediate coating layer of yttria-stabilized zirconia (YSZ) was first deposited onto the PEEK substrates to provide heat shielding during subsequent post-deposition heat treatment to prevent degradation of PEEK substrates and coating/substrate interface. Plasma activation of the PEEK substrate surfaces before deposition resulted in a significant increase in coating adhesion strength. Post-deposition heat treatments of microwave and hydrothermal annealing were studied with the goal of forming crystalline HA without the use of high temperatures required in conventional annealing. Microstructural and compositional analyses by scanning electron microscopy (SEM) and X-ray diffraction revealed that the YSZ layer exhibited a crystalline structure as-deposited, with columnar grains oriented along the growth direction, whereas the HA layer was shown to be amorphous as-deposited. After microwave annealing, the HA coating exhibited a columnar crystalline microstructure, similar to that of the underlying YSZ crystalline layer; XRD analysis confirmed a crystalline HA phase in the coating. It is suggested that the existence of the crystalline YSZ layer aids in the formation of the HA layer upon heating, possibly lowering the activation energy for crystallization by providing nucleation sites for HA grain formation. Cell culture tests showed a significant increase in initial cell attachment and growth on the microwave-annealed coatings, compared with uncoated PEEK and amorphous HA surfaces. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 101A: 2621–2629, 2013.