Consumption of probiotics is known to influence the gut microbiota. The aim of this study was to assess the effect of probiotic powder containing Lactobacillus plantarum Dad-13 on bacterial composition in the gut by examining fecal samples of school-age children in Yogyakarta, Indonesia. This is a randomized, double-blind, placebo-controlled study. A total of 40 healthy subjects were recruited for this study and were divided into two groups: placebo group and probiotic group. The placebo group consumed skim milk and the probiotic group consumed probiotic powder containing L. plantarum Dad-13 (2 × 109 CFU/g) for 65 days. The results showed that placebo intake had no significant effect on gut microbiota; however, probiotic caused a significant increase in L. plantarum and Lactobacillus population, while decreasing the population of E. coli and non-E. coli coliform bacteria by 55% and 75%, respectively and Bifidobacteria count did not change significantly. The study concluded that consumption of probiotic powder L. plantarum Dad-13 could increase propionic acid thereby decreasing the gut pH which has an effect on the microbial population.