The aim of the present study is to eliminate the bioinertness of polyetheretherketone (PEEK) material and to increase its osteogenic activity by applying a number of surface modifications in order to discover the most effective method. First, the surface of the bare PEEK (B-PEEK) was mechanically modified by sandblasting (S-PEEK). As a second method, physical modification was provided by etching of B-PEEK in 10 M sodium hydroxide (NaOH) solution at 60 degrees C for 48 h (N-PEEK). Following the sandblasting, S-PEEK samples were also etched with NaOH to obtain SN-PEEK samples. In order to increase osteogenic activity of the mechanically and/or physically modified PEEK samples, they were coated with boron-doped nanohydroxyapatite (B-nHAp) in the presence of microwave energy. Thus, B-PEEK/B-nHAp, S-PEEK/B-nHAp, N-PEEK/B-nHAp and SN-PEEK/B-nHAp samples were obtained. While water contact angles and surface roughness of the B-PEEK samples increased after modification, hydrophilicity increased with B-nHAp coating. Cell culture results demonstrated that high proliferation and differentiation capacities of MC3T3-E1 cells were obtained on the B-nHAP-coated surfaces compared to uncoated specimens. However, channeled texture of both the N-PEEK and N-PEEK/B-nHAp samples enhanced Col1a1 mRNA expression and collagen secretion in addition to increased alkaline phosphatase (ALP) activity when compared to other groups. As a result, it was determined that the bioactivity increased on the modified PEEK surfaces, but the most effective osteogenic activity was provided with B-nHAp coatings. The synergetic effect of NaOH etching and B-nHAp coatings might be used as a promising surface modification method to use PEEK material in orthopedic and dental applications with increased osteogenic activity.