Purpose: To evaluate the response of human peri-implant soft tissue (PIST) to different healing abutment materials 24 hours after positioning by assessing the expression of genes related to the early connective tissue wound healing response. Materials and Methods: The following four materials were used to create experimental abutments that were mounted on implants placed in five patients (four different abutments in each patient): group A—grade 4 titanium (Ti), group B—grade 5 Ti, group C—zirconia (Zr), and group D—polyetheretherketone (PEEK). Before implant placement, a gingival biopsy (control, CT) sample was obtained using a 2-mm-diameter punch (T0). After 24 hours, PIST biopsy samples were collected using a specifically designed custom-made cutting device. Real-time polymerase chain reaction (PCR) was performed to analyze the expression of the following genes: COL-I, COL-III, MMP-1, TIMP-1, TGF-β1, FN, ITGA4, ITGA5, ITGB1, RAC-1, COL-IV, αSMA, IL-6, and CXCL-1. Results: Gene expression analysis showed some differences between CT and the experimental groups; however, no significant differences were detected when comparing the experimental groups. COL-I was significantly downregulated in groups A and C compared to CT. Expression of MMP-1 and TIMP-1 increased in all the experimental groups but to a lesser extent in group A. FN, RAC-1, COL-IV, and αSMA were downregulated, especially in
group A, in which CXCL-1 and IL-6 showed the lowest expression. Conclusions: The results of grade 4 Ti and Zr abutments seem to be promising, because a lower expression of genes related to inflammation, myofibroblast activation, and extracellular matrix remodeling was observed when compared with grade 5 Ti and PEEK, without triggering a profibrotic response in the early phases of PIST repair.