Aim: To explore the application of the combined use of baseline salivary biomarkers and clinical parameters in predicting the outcome of scaling and root planing (SRP). Materials and methods: Forty patients with advanced periodontitis were included. Baseline saliva samples were analysed for interleukin-1β (IL-1β), matrix metalloproteinase-8 and the loads of Porphyromonas gingivalis, Prevotella intermedia, Aggregatibacter actinomycetemcomitans and Tannerella forsythia. After SRP, pocket closure and further attachment loss at 6 months post-treatment were chosen as outcome variables. Models to predict the outcomes were established by generalized estimating equations. Results: The combined use of baseline clinical attachment level (CAL), site location and IL-1β (area under the curve [AUC] = 0.764) better predicted pocket closure than probing depth (AUC = 0.672), CAL (AUC = 0.679), site location (AUC = 0.654) or IL-1β (AUC = 0.579) alone. The combination of site location, tooth loss, percentage of deep pockets, detection of A. actinomycetemcomitans and T. forsythia load (AUC = 0.842) better predicted further clinical attachment loss than site location (AUC = 0.715), tooth loss (AUC = 0.530), percentage of deep pockets (AUC = 0.659) or T. forsythia load (AUC = 0.647) alone. Conclusion: The combination of baseline salivary biomarkers and clinical parameters better predicted SRP outcomes than each alone. The current study indicates the possible usefulness of salivary biomarkers in addition to tooth-related parameters in predicting SRP outcomes.