Despite the differences in material properties and shapes among the different types of prefabricated titanium (pTiA) and individualized hybrid zirconia abutments (ihZiA), the biological and clinical relevance of materials and construction features remains vague. Yet, individualized ihZiA are increasingly implemented into daily routine aiming to satisfy rising expectations. The objective was to compare these two types of abutments in fixed dental prostheses (FDP). This cross-sectional study examined 462 implants in 102 patients comparing pTiA (52 patients) to ihZiA (50 patients) for FDP. These different treatment regimens were evaluated in terms of peri-implant health, radiographic bone loss, and oral-health related quality of life (OH-QoL) with special consideration of abutment type and superstructure design. ihZiA showed significantly different design features than prefabricated pTiA, but the annual bone loss in both groups did not. Visible titanium in the esthetic zone negatively impacted OHIP 14 scores. The combination of an emergence angle (EA) of < 30° and a concave emergence profile (EP) as well as gingiva thickness (p = 0.002) at the time of the prosthetic restoration significantly improved the annual peri-implant bone loss, independently of the abutment type. ihZiA showed comparable results to pTiA. To optimize the long-term outcome, not just material alone but generating adequate soft tissue thickness, minimizing the EA, and applying a concave EP seem to be the most relevant factors. To improve OH-QoL, particular attention must be paid to the esthetic zone.