AimTo evaluate the effect of cigarette smoking on periodontal health at patient, tooth, and site levels following supportive therapy.Materials and MethodsEighty chronic periodontitis patients, 40 smokers and 40 non‐smokers, were recruited to a single‐arm clinical trial. Periodontal examinations were performed at baseline (T0), 3 months following active periodontal therapy (T1), and 12 months following supportive periodontal therapy (T2). Smoking status was validated measuring serum cotinine levels. Probing depth (PD) ≥ 5 mm with bleeding on probing (BoP) was defined as the primary outcome. Logistic regression analyses adjusted for clustered observations of patients, teeth, and sites and mixed effects models were employed to analyse the data.ResultsAll clinical parameters improved from T0 to T2 (p < 0.001), whereas PD, bleeding index (BI), and plaque index (PI) increased from T1 to T2 in smokers and non‐smokers (p < 0.001). An overall negative effect of smoking was revealed at T2 (OR = 2.78, CI: 1.49, 5.18, p < 0.001), with the most pronounced effect at maxillary single‐rooted teeth (OR = 5.08, CI: 2.01, 12.78, p < 0.001). At the patient level, less variation in treatment outcome was detected within smokers (ICC = 0.137) compared with non‐smokers (ICC = 0.051).ConclusionSmoking has a negative effect on periodontal health following 12 months of supportive therapy, in particular at maxillary single‐rooted teeth.