Streptococcus mutans (S. mutans) is the major pathogen involved in caries development during the first few years of life. Prebiotics represent a breakthrough approach to maintaining oral health by utilizing naturally beneficial bacteria against harmful bacteria. Aim: To assess the effects of prebiotics supplements on salivary pH and salivary buffer capacity in children with early childhood caries (ECC). Materials and methods: This study was performed on 23 samples, aged 3–6 years who received prebiotics supplements for 14 days, followed up to 3 and 6 months. Unstimulated saliva samples were collected to assess salivary pH and salivary buffer capacity using salivary check buffer kit. Statistical analysis used: The data showed normal distribution; hence, parametric tests were applied. Repeated measures of analysis of variance were applied to compare the mean at the three different time intervals, followed by paired t-test for pairwise comparison. Results: There was a highly significant difference on comparing the different parameters. Salivary pH was lowest at baseline with a mean value of 6.65 which increased at the 3–6-month follow-up to 7.00 and 7.33. Similarly, salivary buffer capacity which was 4.73 at baseline, increased at 3 months to 8.17, and at 6 months to 10.34. Conclusion: It can be suggested that prebiotics supplements can be adopted as a novel approach in children with ECC as a form of preventive measure to facilitate a better lifestyle. Clinical significance: These prebiotics when taken for a period of 2 weeks increased the salivary pH as well as salivary buffer capacity when the data was compared at different time intervals emphasizing its importance, especially in children with ECC.