Amorphous PEEK coating was prepared on Al substrate, employing flame spraying technology. The amorphous coating was subjected to annealing treatments under different conditions. Both differential scanning calorimetry (DSC) and wide angle X-ray diffraction (WAXD) analysis revealed that the isothermally treated coating exhibited semi-crystalline structure. Coexistence of double crystal entities in semi-crystalline PEEK coating was deduced from the results obtained by DSC and WAXD measurements. Annealing temperature and holding time under this temperature affect the morphology of the minor crystal entity which is metastable. The mechanical properties of the isothermally treated coating were investigated considering coating microhardness and friction and wear properties. The variations of the coating mechanical properties were correlated with the modifications in the coating structure induced by the different annealing conditions.