Stunting, a form of malnutrition, has become a global challenge affecting approximately 148 million children under the age of five worldwide, with Indonesia recording a prevalence rate of 21.5% in 2023. The first 1,000 days of life (HPK) are considered a critical phase in the formation of the gut microbiome, which plays a decisive role in children's linear growth patterns. A mother's diet during pregnancy and breastfeeding has been identified as a key factor in shaping the composition of an infant's gut microbiota; however, understanding of the mechanisms and evidence-based interventions—both in a global context and in Indonesia—remains limited. This study aims to analyze the impact of maternal diet on the formation of the infant gut microbiome, identify the biological mechanisms linking dysbiosis to stunting, and evaluate the effectiveness of microbiome-based interventions in stunting prevention efforts. A systematic literature search was conducted in five scientific databases (PubMed, Scopus, ScienceDirect, SpringerLink, and Google Scholar) to identify articles published between 2021 and 2026 in English or Indonesian. A total of 27 articles met the inclusion criteria. A varied maternal diet rich in fiber, omega-3, and zinc increases the diversity of the breast milk microbiome and promotes the dominance of Bifidobacterium in the infant's digestive tract. Dysbiosis, characterized by a decrease in Bifidobacterium and Faecalibacterium prausnitzii, was significantly correlated with stunting via the Environmental Enteric Dysfunction pathway, reduced SCFAs, and disruption of the gut-IGF-1 axis. Supplementation with the probiotic Lactobacillus rhamnosus GG and synbiotic was shown to significantly improve HAZ scores in children with stunting. Maternal diet is a key modifiable factor in shaping the infant gut microbiome during the first 1,000 days of life, and microbiome-based interventions hold promise as therapeutic and preventive strategies for stunting.