AimThe aim of this retrospective long‐term follow‐up of a 3‐month RCT was to assess whether non‐surgical peri‐implantitis treatment with adjunctive systemic antibiotics influenced the need for additional surgical treatment.Materials and MethodsPatients enrolled in an aftercare programme following non‐surgical peri‐implantitis treatment, with or without systemic amoxicillin and metronidazole, were analysed. Data had previously been collected pre‐treatment (T0) and 3 months after treatment (T1) and were additionally collected during subsequent aftercare visits, until the final assessment (T2). Primary outcome was the need for additional surgical peri‐implantitis therapy during the aftercare programme, analysed via Kaplan–Meier analysis and Cox regression. Secondary outcomes involved clinical parameters, assessed using parametric and non‐parametric tests.ResultsForty‐five patients (22 AB− group, 23 AB+ group) were included. The mean follow‐up time between T1 and T2 was 35.9 months (SD = 21.0). 73.9% of the AB+ group and 50.0% of the AB− group did not receive additional surgical therapy (log‐rank test, p = .110). The adjusted Cox regression model did not provide a significant result for antibiotics (β = .441, 95% CI = 0.159–1.220, p = .115). Univariable regression analysis highlighted the influence of baseline peri‐implant pocket depth on the need for surgical treatment (β = 1.446, 95% CI = 1.035–2.020, p = .031).ConclusionsSystemic amoxicillin and metronidazole administered during non‐surgical peri‐implantitis treatment do not seem to prevent the need for additional surgical therapy in the long term, during a structured aftercare programme.