<p>Korean fermented soybean pastes (jang, including doenjang, ganjang, and gochujang) and jeotgal are characterized by their complex microbial ecosystems, rich nutrient composition, and notable health-promoting properties. These foods naturally generate bioactive metabolites such as isoflavones, γ-polyglutamic acid, phenolic acids, and peptides, which contribute to antioxidant, anti-inflammatory, anti-cancer, and menopausal symptom-alleviating effects. Unlike standardized industrial products, traditional fermentation relies on spontaneous microbial interactions and extended maturation, resulting in distinctive metabolite profiles and enhanced functional activity. Recent advances in metabolomics have enabled comprehensive characterization of these metabolites through both targeted and untargeted approaches, offering insights into fermentation dynamics, nutritional quality, and functional potential. Comparative metabolomic studies reveal that traditionally fermented soybean pastes and jeotgal exhibit greater chemical diversity and bioactivity compared with their commercial counterparts, emphasizing both their scientific and cultural value. This review synthesizes current evidence on the nutritional and functional attributes of these foods, with a focus on metabolomic methodologies that elucidate key metabolic pathways and their physiological relevance. In addition, it highlights the industrial potential of fermentation-derived bioactive compounds, while emphasizing the need for integrative multi-omics strategies, including genomics and metagenomics, to understand complex microbe–host–metabolite interactions. Such approaches can deepen understanding of how fermentation-derived metabolites contribute to host health, gut microbiota modulation, and disease prevention. By consolidating nutritional, functional, and metabolomic perspectives, this review provides a focused framework for advancing the global recognition, scientific validation, and sustainable development of Korean fermented soybean pastes and jeotgal.</p>