The present study investigated the ingestion effect of chocolate probiotic containing Dad-13 in undernourished children. A 100-day observation was conducted on undernourished children in Lombok, who were divided into probiotic ( = 28) and placebo ( = 28) groups. Fecal sampling was performed on the 10 and 100 days and further analyzed for gut microbiota composition, short-chain fatty acid (SCFA), and fecal pH. A significant difference was found in the diversity index, fecal pH, and several microbiotas at the phylum and genus levels. At the phylum level, was significantly higher in the probiotic group, and a higher relative abundance (RA) of was found in the placebo group. At the genus level, significant differences were observed in some bacteria, such as and . Therefore, it can be concluded that the probiotic intervention in this study resulted in changes of gut microbiota diversity and fecal pH. Thai Clinical Trials Registry identifier: TCTR20220425001.