Background/Objectives: Conventional logistic regression is widely used in the field of dentistry, specifically for prediction purposes in longitudinal studies. This study aimed to compare the validity of different supervised machine learning (ML) models to the conventional logistic regression (LR) model to predict the outcomes of nonsurgical periodontal treatment (NSPT). Methods: Patients diagnosed with periodontitis received full periodontal charting, including bleeding on probing (BoP), probing pocket depth (PPD), and clinical attachment loss (CAL). Furthermore, the tooth type, tooth location, tooth surface, arch type, and gingival phenotype were also collected as site-specific predictors. Later, root surface debridement was provided and treatment outcomes were evaluated after 3 months. Site-specific predictors were used to train five ML models, including random forest (RF), decision tree (DT), support vector classifier (SVC), K-nearest neighbors (KNN), and Gaussian naïve Bayes (GNB), to develop predictive models. Results: Site-specific predictors of 1108 examined sites were used, and the overall accuracy prediction of the conventional LR model was 70.4%, with PPD statistically significantly associated with the outcome of NSPT (odds ratio = 0.577, p = 0.001). Among the ML models examined, only GNB and SVC showed comparable prediction accuracy (71.0% and 70.4%, respectively) to the LR model, whereas the prediction accuracies of KNN, RF, and DT were 65.0%, 62.0%, and 61.0%, respectively. Similarly, baseline PPD was shown to be the most important featured predictor by both the RF and DT models. Conclusions: The evidence suggests that supervised ML models do not outperform the LR model in predicting the outcomes of NSPT. A larger sample size and more predictors of periodontitis are necessary to enhance the accuracy of ML models over the LR model in predicting the outcomes of NSPT.