Despite high success rates of dental implants, surface exposure may occur as a consequence of biologic width establishment associated with surgery. This prospective split-mouth study evaluated the effect of early implant surface exposure caused by initial bone remodeling on long-term peri-implant bone stability and peri-implant health. Additionally, Oral Health-Related Quality of Life (OHRQoL) was assessed by means of the Oral Health Impact Profile-14 (OHIP-14). Twenty-six patients received two non-splinted implants supporting an overdenture in the mandible by means of locators. One implant was installed equicrestally (control) and the second one was installed subcrestally, taking at least 3 mm soft tissue thickness into account (test). During initial bone remodeling (up to 6 months postoperatively), equicrestal placement yielded 0.68 mm additional surface exposure compared to subcrestal placement (p < 0.001). Afterwards, bone level and peri-implant health were comparable in both treatment conditions and stable up to 5 years. The implant overdenture improved OHRQoL (p < 0.01) and remained unchanged thereafter (p = 0.51). In conclusion, adapting the vertical position of the implant concerning the soft tissue thickness prevents early implant surface exposure caused by initial bone remodeling, but in a well-maintained population, this has no impact on long-term prognosis. The treatment of edentulousness with an implant mandibular overdenture improves OHRQoL.