BackgroundN‐terminal portion of the B‐type natriuretic propeptide (NT‐proBNP) has potentially been shown to play an important role in the development of periodontitis and cardiovascular disease (CVD). This study evaluated the efficacy of periodontal treatment on NT‐proBNP and related CVD biomarkers and explored whether subjects harboring high NT‐proBNP at baseline showed increased clinical benefits with the non‐surgical periodontal treatment performed with full‐mouth scaling and root planing (FM‐SRP) at 6‐month follow‐up.MethodsForty‐eight patients with stage III periodontitis were randomized to receive minimal standard oral care (SOC) (n = 24) or FM‐SRP (n = 24) protocol. Clinical periodontal parameters (probing depth, clinical attachment loss, bleeding on probing), serum NT‐proBNP, α1‐antitrypsin, C‐reactive protein (hs‐CRP), endothelial cell‐specific molecule‐1 (ECM‐1), and neutrophil gelatinase‐associated lipocalin (NGAL) concentrations were assessed at baseline and at 1‐, 3‐, and 6‐ month follow‐up.ResultsAt 6 months, FM‐SRP was more effective than SOC in reducing periodontal parameters and mean proportions of NT‐proBNP (p = 0.004), hs‐CRP (p = 0.003), α1‐antitrypsin (p = 0.012), ECM‐1 (p = 0.014), and NGAL (p = 0.045). At 6‐month follow‐up, the reduced NT‐proBNP, α1‐antitrypsin, hs‐CRP, ECM‐1, and NGAL levels were significantly correlated with the extent of periodontitis (p < 0.05). Furthermore, the analysis of variance analysis evidenced that, at 6‐month follow‐up, FM‐SRP significantly impacted the reduction of NT‐proBNP, hs‐CRP, ECM‐1, and NGAL. Moreover, high levels of NT‐proBNP, hs‐CRP, ECM‐1, and NGAL at baseline significantly influenced the efficacy of periodontal treatment positively.ConclusionIn this study, FM‐SRP was more effective than SOC in reducing clinical variables and NT‐proBNP levels, although subjects who harbored high NT‐proBNP concentrations at baseline showed greater clinical benefits of periodontal treatment at 6‐month follow‐up.