Polyetheretherketone (PEEK) is a biocompatible, chemically and physically stable radiolucent polymer that exhibits a similar elastic modulus to the normal human bone, making it an attractive orthopedic implant material. However, PEEK is biologically inert, preventing strong enough bonding with the surrounding bone tissue when implanted in vivo. Surface modification and composite preparation are the two main strategies for the improvement of the bioactivity of PEEK. In this study, the plasma activated PEEK surfaces with the embedded bioglass, chitosan, and bioglass-chitosan mixed layers applying from the solution dip-coating technique were investigated. The most prominent factors affecting the coating biocompatibility are strictly connected with the composition of its outer surface (its charge and functional groups), hydrophilic-hydrophobic character, wettability and surface free energy, and topography (size of pores/substructures, roughness, stiffness), as well as the personal characteristics of the patient. The obtained surfaces were examined in terms of wettability and surface-free energy changes. Additionally, FTIR (Fourier Transformation Infrared Spectrometry) and SIMS (Secondary Ion Mass Spectrometry) were applied to establish and control the coating composition. Simultaneously the structure of coatings was visualized with the aid of SEM (Scanning Electron Microscopy). Finally, the obtained systems were incubated in SBF (Simulated Body Fluid) to verify the modifications’ influence on the bioactivity/biocompatibility of the PEEK surface. Different structures with variable compositions, as well as changes of the wettability, were observed depending on the applied modification. In addition, the incubation in SBF suggested that the bioglass-chitosan ratio influenced the formation of apatite-like structures on the modified PEEK surfaces.