Background: Seventy-two percent of 12-year-old children in Indonesia experience dental caries, among 10–14-year-olds is 73%, and in 15-year-olds is 68.5%. Islamic boarding schools (pesantren) are one of the educational institutions in Indonesia, and dental caries status among the school students is moderate to severe. A preventive approach according to ecological balance has been proposed to prevent oral cavity disorders, especially dental caries. Objectives: This study aimed to investigate the correlation of probiotic consumption with plaque index, salivary pH, and quantification. Method: This research has been done at the Ibnu Hajar boarding school. A total of 40 research subjects aged 12–15 years were allocated into two groups (treatment and control), each consist of 20 subjects. Children in the treatment group took one probiotic lozenge daily. Saliva samples of the subjects were taken at baseline and 7th days. Plaque index, salivary pH, and quantification measurements were done before and after consumption of the probiotic. Statistical analyses used the T-test and Spearman correlation test. Results: There was a significant difference in plaque index, saliva pH, and an insignificant difference in quantification after consuming the probiotics. The correlation coefficient between probiotics consumption and plaque index is 0.672, between probiotic consumption and salivary pH is r = 0.433 ( < 0,05), while between probiotic consumption and quantification is 0.162 ( > 0,05). Conclusion: A significant correlation between probiotic consumption with plaque index and salivary pH was found, but the correlation with quantification was found insignificant.