Polyetheretherketone (PEEK) is an alternative to metallic implants and a material of choice in many applications, including orthopedic, spinal, trauma, and dental. While titanium (Ti) and Ti-alloys are widely used in many intraosseous implants due to its biocompatibility and ability to osseointegrate, negatives include stiffness which contributes to shear stress, radio-opacity, and Ti-sensitivity. Many surgeons prefer to use PEEK due to its biocompatibility, similar elasticity to bone, and radiolucency, however, due to its inert properties, it fails to fully integrate with bone. Accelerated Neutral Atom Beam (ANAB) technology has been successfully employed to demonstrate enhanced bioactivity of PEEK both in vitro and in vivo. In this study, we further characterize surfaces of PEEK modified by ANAB as well as elucidate attachment and genetic effects of dental pulp stem cells (DPSC) exposed to these surfaces. ANAB modification resulted in decreased contact angle at 72.9 ± 4.5° as compared to 92.4 ± 8.5° for control (p < 0.01) and a decreased average surface roughness, however with a nano-textured surface profile. ANAB treatment also increased the ability of DPSC attachment and proliferation with considerable genetic differences showing earlier progression towards osteogenic differentiation. This surface modification is achieved without adding a coating or changing the chemical composition of the PEEK material. Taken together, we show that ANAB processing of PEEK surface enhances the bioactivity of implantable medical devices without an additive or a coating.