Purpose: To explore the comparative efficacy of two different drilling protocols that use burs with different designs to help prepare implant sites through the evaluation of radiographic, clinical, and patient-reported outcomes. Materials andMethods: The present randomized controlled clinical trial, with an allocation ratio of 1:1, was carried out at the University of Milan and at the IRCCS Ospedale Galeazzi Sant’Ambrogio Hospital in Milan by two experienced surgeons and researchers (S.C. and S.T.). In the control group, surgeons followed a protocol with standard straight burs, and in the test group they used step burs. In both groups the patients received the same type of implants and prostheses. The primary outcome was marginal bone resorption 1 year after prosthetic placement. Results: The study included and treated a total of 60 patients (86 implants). At the 1-year follow-up, 54 patients (74 implants) were screened, and 50 patients were screened at the 2-year follow-up (69 implants). This study showed no evidence of a difference in bone resorption, which increased significantly over time, between the control and test groups. Conclusions: Bot clinical parameters and patient-centered outcomes revealed no differences between the two protocols for implant site preparation with two different drill shapes.