The purpose of this research is to compare the cytotoxicity of polyetheretherketone (PEEK) and polyetherketoneketone (PEKK) with conventional dental implant–abutment materials, namely titanium alloy (Ti-6Al-4V) and yttria-stabilized tetragonal zirconia polycrystal (Y-TZP), to evaluate the cell metabolic activity, cytotoxicity, and inflammation potential of human oral fibroblasts (HOF) on these materials. Disk-shaped specimens were designed and prepared via a dental computer-aided manufacturing technology system. Surface topography, roughness, and free energy were investigated by atomic force microscope and contact angle analyzer; cell metabolic activity and cytotoxicity by MTT assay; and morphological changes by scanning electron microscopy (SEM). The effect of pro-inflammatory gene expression was evaluated by RT-qPCR. The obtained data were analyzed with one-way analysis of variance and post-hoc Tukey’s honest significant difference tests. PEEK and PEKK exhibited higher submicron surface roughness (0.04 μm) and hydrophobicity (>80°) than the control. Although the cell activity of PEEK was lower than that of Ti-6Al-4V and Y-TZP for the first 24 h (p < 0.05), after 48 h there was no difference (p > 0.05). According to the cell cytotoxicity and the pro-inflammatory cytokine gene expression assays, there was no difference between the materials (p > 0.05). SEM observations indicated that HOF adhered poorly to PEKK but properly to Ti-6Al-4V, Y-TZP, and PEEK. PEEK and PEKK show comparable epithelial biological responses to Ti-6Al-4V and Y-TZP as implant–abutment materials. Between the two polymeric materials, the PEEK surface, where the HOF showed better cell metabolic activity and cytotoxicity, was a more promising implant–abutment material.