Flame sprayed PEEK (poly-ether-ether-ketone) coatings, with an amorphous structure, were subjected to isothermal treatments with annealing temperatures from 180 to 300 °C and holding time from 1 to 30 min. The coating structures were studied by means of DSC (Differential Scanning Calorimetry) and XRD (X-Ray Diffraction) analyses. All annealed coatings exhibit semi-crystalline structures. Coexistence of thick and thin lamellae in the spherulites of annealed coatings can be deduced from the analysis results. The Knoop hardness and the interfacial adhesion of the coatings were examined. The annealed coatings exhibit higher hardness than the amorphous ones. The formation of the thick lamellae is the determinant factor for improving the coating hardness. However, the annealed coatings exhibit a weak adherence to the substrate. Some fissures or spherical porosities could be observed, in certain zones, on the coating/substrate interface. The formation of these fissures and porosities could be ascribed to the coating residual stress and the big volume contraction during the crystallisation that occurred under the annealing condition.