Objectives: This retrospective study aimed to evaluate peri-implant marginal bone level changes and radiographic grayscale value (GSV) alterations in vertically compromised bone around ultra-short implants (5.2 mm) placed in native bone compared to standard-length implants (8–14 mm) placed in augmented sites. Methods: The mean follow-up period was 38 months, with a maximum of 64 months. A total of 53 patients, collectively receiving 131 implants, were included. Each patient received at least both one ultra-short implant and one standard-length implant. In total 78 short implants and 53 standard length implants were placed. Standard-length implants were predominantly placed using alveolar ridge augmentation with autologous bone chips, sinus lifting, or retromolar bone block grafting. Autologous bone chips were supplemented with up to 50% bone substitute materials. Peri- implant marginal bone levels were assessed using the Distance Implant to Bone (DIB) method, while radiographic GSV served as a surrogate for bone density. All radiographic measurements were performed by two blinded evaluators using an automated x-ray overlay protocol, achieving high inter-rater reliability (intraclass correlation coefficients > 0.98). A linear mixed model, accounting for heterogeneous follow-up intervals, was applied to estimate changes in marginal bone levels (ΔMBL) and grayscale values (ΔGSV) (p < 0.05). Results: The mean follow-up period was 38 months, with a maximum of 64 months. A total of 123 implants were assessed for changes in marginal bone level and grayscale values, representing bone density. Ultra-short implants demonstrated significantly lower marginal bone loss over the observation period (ΔMBL = −0.61 ± 0.93 mm) than standard-length implants placed in augmented bone (ΔMBL = −1.11 ± 1.26 mm; p = 0.001). Moreover, ∆GSV around ultra-short implants significantly increased (ΔGSV = 3.26 ± 20.52 a.u), whereas standard-length implants exhibited a decrease in radiographic density (ΔGSV = −0.76 ± 21.59 a.u; p = 0.009). Conclusions: Within the limitations of this mid-term retrospective study, ultra-short implants placed in native bone exhibited statistically superior marginal bone preservation and significantly increased radiographic density when compared to standard-length implants placed in augmented sites. These results help to underscore the potential clinical advantage of opting for ultra-short implants in suitable native bone conditions to reduce the morbidity associated with extensive augmentation and less risk for periimplantitis on the long-term run in selected cases. Nevertheless, further long term, randomized investigations are warranted to confirm these findings.