Objectives The aim of this study was to assess the long-term efficacy of reconstructive treatment of peri-implantitis intraosseous defects. Material and Methods Peri-implant intraosseous defects were augmented using either an autogenous bone graft (AB) or a bovine-derived xenograft (BDX) in combination with a collagen membrane. Maintenance was provided every third month. Results In the AB group, 16 patients with 25 implants remained at year five. In the BDX group, 23 patients with 38 implants remained. Between baseline and year 5, bleeding on probing (BOP) and probing pocket depth (PPD) scores were reduced in both groups (p < .001). In the AB and BDX groups, mean PPD between baseline and year five was reduced by 1.7 and 2.8 mm, respectively. The difference between groups was significant (p < .001). In the AB group, the mean bone level change at implant level between baseline and years three and five was-0,2 and -0.7 mm, respectively. In the BDX group, the mean bone level change at implant level between baseline and years three and five was 1.6 and 1.6 mm, respectively. The difference between the groups was significant (p < .001). Successful treatment (no bone loss, no probing pocket depth (PPD) > 5 mm, no suppuration, maximum one implant surface with bleeding on probing (BOP) at year five) was obtained in 9/25 implants (36%) in the AB group and in 29/37 implants (78.3%) in the BDX group. Conclusions Reconstructive surgical treatment of peri-implant defects using BDX resulted in more predictable outcomes than using autogenous bone over 5 years.