Improving soft tissue attachment to implant abutments is a crucial factor for enduring health and maintenance of soft peri-implant tissue health. In this in vitro study we aimed to compare the biocompatibility of three different abutment surfaces: titanium, zirconia and modified polyetheretherketone (PEEK). Surface topography, roughness and wettability were investigated with scanning electron microscopy, profilometer and contact angle meter, respectively. Human gingival epithelial keratinocytes were examined for viability, morphology, proliferation and migration by using tetrazolium salt colorimetric assay, scanning electron microscopy imaging, immunofluorescence bromodeoxyuridine analysis and scratch wound healing assays. Roughness measurements revealed differences between the investigated surfaces. Keratinocytes cultured on all examined surfaces indicated adhesion and attachment by means of scanning electron microscopy imaging. Cell viability assays showed no significant differences between the groups (p > 0.05). The modified PEEK surface similarly improved surface roughness in comparison to titanium and zirconia, which resulted in greater and equivalent cell proliferation and migration. The study methodology showed here may emphasize the importance of cell interactions with different abutment materials, which in part increases the changes of implant success. PEEK, titanium and zirconia surface types used in this study showed mostly similar epithelial biological responses.