Early marginal bone loss (MBL) is a non-infective remodeling process of variable entity occurring within the first year after implant placement. It has a multifactorial etiology, being influenced by both surgical and prosthetic factors. Their impact remains a matter of debate, and controversial information is available, particularly regarding implants placed subcrestally. The present multicenter prospective clinical study aimed to correlate marginal bone loss around platform-switched implants with conical connection inserted subcrestally to general and local factors. Fifty-five patients were enrolled according to strict inclusion/exclusion criteria by four clinical centers. Single or multiple implants (AnyRidge, MegaGen, South Korea) were inserted in the posterior mandible with a one-stage protocol. Impressions were taken after two months of healing (T1), screwed metal-ceramic restorations were delivered three months after implant insertion (T2), and patients were recalled after six months (T3) and twelve months (T4) of prosthetic loading. Periapical radiographs were acquired at each time point. Bone levels were measured at each time point on both mesial and distal aspects of implants. Linear mixed models were fitted to the data to identify predictors associated with MBL. Fifty patients (25 male, 25 female; mean age 58.0 ± 12.8) with a total of 83 implants were included in the final analysis. The mean subcrestal position of the implant shoulder at baseline was 1.24 ± 0.57 mm, while at T4, it was 0.46 ± 0.59 mm under the bone level. Early marginal bone remodeling was significantly influenced by implant insertion depth and factors related to biological width establishment (vertical mucosal thickness, healing, and prosthetic abutment height). Deep implant insertion, thin peri-implant mucosa, and short abutments were associated with greater marginal bone loss up to six months after prosthetic loading. Peri-implant bone levels tended to stabilize after this time, and no further marginal bone resorption was recorded at twelve months after implant loading.