Background: Implant replacement is among the treatment options for severe peri-implantitis. The aim of this single-cohort study was to evaluate the feasibility of replacing compromised implants affected by advanced peri-implantitis with new implants with a porous trabecular metal (TM) structure. Materials and Methods: Patients with one or more implants in the posterior region showing a defect depth >50% of implant length, measured from the residual crest, were consecutively included. Two months after implant removal, patients received a TM implant combined with a xenograft and a resorbable membrane. The implant stability quotient (ISQ) was measured at placement and re-assessed five months later (at uncovering), then after 6, 12, and 24 months of function. Marginal bone loss was radiographically evaluated. Results: Twenty consecutive cases were included. One patient dropped out due to COVID-19 infection, and nineteen cases were evaluated up to 24 months. At placement, the mean ISQ was 53.08 ± 13.65 (standard deviation), which increased significantly to 69.74 ± 9.01 after five months of healing (p < 0.001) and to 78.00 ± 7.29 after six months of loading (p < 0.001). Thereafter, the ISQ remained stable for up to 24 months (80.55 ± 4.73). All implants successfully osseointegrated and were restored as planned. After two years, the average marginal bone level change was −0.41 ± 0.38 mm (95% confidence interval −0.60, −0.21), which was limited yet significantly different from the baseline (p < 0.05). Conclusions: The treatment of advanced peri-implant defects using TM implants inserted two months after explantation in combination with guided bone regeneration may achieve successful outcomes up to two years follow-up, even in the presence of low primary stability.