The objectives of this study were to identify risk factors associated with the premature cover screw exposure (pCSE) at dental implants and to evaluate the influence of a pCSE on peri-implant marginal bone level (MBL) change compared to non-exposed implants. Retrospective data assessment from 165 patients (mean age=54.0±14.4years) who received 395 submerged implants included demographic, health-related, and therapeutic variables which were analyzed for their respective impact. MBL change was detected at digital radiographs obtained from first- and second-stage surgeries. pCSE were detected in 43 patients (26.1%) and 53 implants (13.4%). An increased frequency of exposure was significantly associated with (I) male gender (p=0.012) at patient level and (II) the posterior region of the jaws (p=0.005), implant systems with platform-matching cover screws, and a vertical distance of ≥0.5mm between bone crest and the implant platform (both p<0.001) at implant level. The decrease in mesial, distal, and total MBL differed significantly (mean total=0.8±0.7 vs. 0.3±0.5; mean mesial=0.8±0.8 vs. 0.3±0.6; mean distal=0.8±0.8 vs. 0.3±0.6mm; p<0.001) between non-exposed and pCSE implants. Male patients, implants with platform-matched cover screws, or when placed supracrestally or in posterior sites revealed significantly more pCSE, resulting in significantly decreased peri-implant MBL compared with non-exposed implants. Patients with an enhanced risk of pCSE should follow frequent regular recalls during the healing period to enable for early diagnosis and intervention.