The aim of this cohort study was to investigate the relationship between crestal bone levels and crown-to-implant ratio of ultra-short implants, after functional loading. 60 patients with single or partial edentulism and alveolar bone atrophy were enrolled and treated between December 2009 and January 2016. Without using bone-grafting procedures, patients were rehabilitated with ultra-short implants characterized by a micro-rough surface and a 6-mm length. Clinical and anatomical crown-to-implant (C/I) ratios and crestal bone levels (CBL) were measured after a follow-up period ranging from 12 to 72 months; all peri-implant and prosthetic parameters were recorded. The data collected were statistically analyzed (p = 0.05). A total of 47 patients with 66 ultra-short implants were completely followed up according to described protocol. The mean follow-up was 48.5 ± 19.1 months. The mean anatomical C/I ratio was 2.2, while the mean clinical C/I ratio was 2.6 ± 0.6 at the baseline and 2.8 ± 0.6 at the last follow-up appointment. Mean CBL as calculated at the baseline was 0.7 ± 0.5 mm, while at the last appointment it measured 1.0 ± 0.5 mm. The overall implant-based success rate was 96.9%, and the mean peri-implant bone loss (PBL) was 0.3 ± 0.3 mm. No statistically significant relationship was found between anatomical or clinical C/I ratio and PBL. Ultra-short implants appear to offer a predictable solution for implant-prosthetic rehabilitation in patients with edentulism and bone atrophy. A high percentage of implants were successful, with minimal crestal bone loss. The high C/I ratio did not appear to influence either peri-implant bone loss or prosthetic complication rates.