Purpose: To complete a reanalysis study of two similarly designed prospective controlled studies exploring prognostic factors associated with the surgical outcomes of reconstructive treatment of peri-implantitis. Materials and Methods: Individual patient data of both studies were gathered. The initial study employed a submerged healing approach via primary wound closure with implant suprastructure removal and complete coverage of grafted sites. The second study employed a nonsubmerged healing protocol in which healing abutments were kept in place and the implants were not fully submerged. Both studies measured all prognostic factors at similar time points throughout 1 year and included clinical defect fill (DF) and radiographic defect fill (RDF), reduction of pocket depth (PDR), and bleeding on probing (BoP). Multilevel regression was used for statistical assessment of outcomes relative to the impact of site, local, surgical, and patient-related variables. Results: Overall, 59 implants (30 submerged and 29 nonsubmerged) were treated. Statistically significant higher DF (on average 0.9 mm higher), RDF (1.7 mm), and PDR (1.3 mm) were observed when a submerged reconstructive approach was performed, whereas BoP reduction was similar. After controlling for treatment (submerged/ nonsubmerged), there were no other significant associations with patient-related (age, sex, smoking, prior periodontitis etc), or implant-related (previous prosthesis type, arch, keratinized tissue width [KTW], etc) factors. Conclusions: Within the study’s limitations, we conclude that a submerged reconstructive approach for surgical management of peri-implantitis leads to significantly enhanced clinical and radiographic outcomes when compared to a nonsubmerged approach.