Indigenous fermented foods represent complex microbial ecosystems shaped by centuries of traditional knowledge, harboring diverse microorganisms with functional traits that extend beyond food transformation to offer considerable potential for sustainable agriculture. This review synthesizes current knowledge on the microbial diversity of traditional fermented foods and examines the metabolic capabilities of resident microorganisms, with emphasis on their prospective integration into agro-ecological systems. Culture-independent metagenomic analyses have revealed that fermented food matrices harbor consortia of lactic acid bacteria, yeasts, Bacillus species, molds, and acetic acid bacteria exhibiting substrate-specific and geography-driven distribution patterns. These microorganisms produce an array of functional metabolites including organic acids, hydrolytic enzymes, exopolysaccharides, and antimicrobial compounds that contribute to both food preservation and potential agricultural applications. Fermentation-derived microorganisms demonstrate plant growth-promoting traits encompassing nitrogen fixation, phosphate solubilization, phytohormone production, and biocontrol against phytopathogens through mechanisms including antibiosis, competition, and induced systemic resistance. The integration of indigenous fermentation microbes into sustainable agriculture through biofertilizers, biopesticides, and soil amendments aligns with circular bioeconomy principles while enhancing nutrient bioavailability and reducing post-harvest losses in food systems. Challenges including microbial variability, safety standardization, and scaling of traditional processes necessitate integrated approaches combining omics-based characterization with participatory research frameworks. Future prospects involve precision fermentation technologies, tailored microbial consortia development, and policy frameworks supporting the translation of indigenous microbial resources into regenerative agricultural practices, thereby bridging food fermentation microbiology with agro-ecological sustainability.