Objectives To investigate whether xenograft EB (EndoBon) is non‐inferior to xenograft BO (Bio‐Oss) when used in reconstructive surgery of peri‐implant osseous defects. Materials and methods Dental patients with one implant each demonstrating peri‐implantitis were randomized to receive surgical debridement and defect fill with either BO or EB. Changes in bone level (BL) and intrabony defect depth (IDD) evaluated radiographically were the primary outcomes. The secondary outcomes included changes in probing pocket depth (PPD), bleeding on probing (BoP), and suppuration on probing (SoP). All outcomes were recorded before treatment and at 6 and 12 months post‐treatment. Results Twenty‐four patients (n = 11 BO, n = 13 EB) completed the study. Both groups demonstrated significant within‐group improvements in all clinical and radiographic parameters at 6 and 12 months (p ≤ .001). At 12 months, both groups presented with IDD reductions of 2.5–3.0 mm on average. The inter‐group differences were not statistically significant at all time points and for all the examined parameters (p > .05). While the radiographic defect fill in both groups exceeded > 1 mm and can be considered treatment success, successful treatment outcomes as defined by Consensus Reporting (no further bone loss, PPD ≤ 5 mm, no BOP, and no SoP) were identified in 2/11 (18%) BO and 0/13 (0%) EB individuals (Fisher's exact test, p = .199). Conclusions Within the limitations of this pilot study, the application of xenograft EB showed to be non‐inferior to xenograft BO when used in reconstructive surgery of peri‐implant osseous defects.