This study employed metagenomics and metabolomics to evaluate the impact of Tetragenococcus halophilus and Zygosaccharomyces rouxii on microbiota composition and metabolite profiles in secondary fortified fermented soy sauce. The Co-culturing of T. halophilus T10 and Z. rouxii QH-1(T1Z) enriched microbial diversity and promoted the proliferation of functional species, thereby enhancing biomarker species. Annotations matched from EggNOG, KEGG, and CAZy databases underscored the significance of carbohydrate and amino acid metabolism in moromi. Sample T1Z enhanced the metabolism by increasing the abundance and catalytic efficiency of the relevant enzymes, resulting in increases of 3.94%, 2.69%, and 11.14%, respectively, with total nitrogen, amino acid nitrogen, and free amino acids. It introduced 11 volatile compounds and increased the alcohol content by 13.65%, and the aldehyde content by 49.28%, while also suppressing the accumulation of ammonium nitrogen and biogenic amines. Metabolic pathway analysis identified Staphylococcus gallinarum, Mammaliicoccus sciuri, and certain Bacillus species, especially B. parathracis, B. velezensis, and B. subtilis, as principal contributors to carbohydrate and amino acid metabolism. These findings offer insight into microbial strain selection for industrial fermentation and provide a foundation for optimizing the process through co-culture bioaugmentation to enhance and underscore the potential of modern microbial techniques in traditional practices.