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Gestational diabetes mellitus (GDM) is a common pregnancy complication with profound short- and long-term consequences for both mother and offspring. Beyond transient hyperglycemia, GDM represents a multifactorial metabolic condition shaped by the interplay of genetic predisposition, epigenetic regulation, and alterations in the maternal microbiome. Dysbiosis of the gut and reproductive tract microbiota contributes to inflammation, insulin resistance, and dyslipidemia during pregnancy, while microbial metabolites influence placental physiology and epigenetic remodeling of key metabolic and imprinted genes. These modifications, including changes in DNA methylation and non-coding RNA expression, link maternal hyperglycemia and microbial shifts to persistent alterations in gene expression that affect trophoblast activity, fetal growth trajectories, and long-term metabolic risk in offspring. Vertical transmission of maternal microbiota further imprints the neonatal microbiome, establishing an early-life foundation for reproductive and metabolic health. Although current diagnostic criteria and biomarkers remain inconsistent across populations, recent advances highlight the microbiome-epigenome axis as a promising source of predictive markers and therapeutic targets. Interventions such as probiotics, prebiotics, synbiotics, and dietary modulation show potential for improving maternal glycemic control, shaping placental function, and modulating fetal programming, although evidence for long-term efficacy is still emerging. Viewing GDM as both a metabolic stress test and a window of reproductive opportunity underscores the importance of early diagnosis and precision strategies. Integrating microbiome research and epigenetic insights into clinical practice offers new avenues to improve maternal outcomes, optimize fetal development, and reduce the intergenerational transmission of reproductive and metabolic disease risk.