Despite the widespread use of bioinoculants to improve crop productivity, their combined influence on seed metabolic composition and nutritional quality, especially through coordinated changes in primary and secondary metabolism, remains poorly understood. In this work, we investigated the individual and synergistic effects of plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on the metabolic profile, antioxidants, and ionic composition of soybean seeds. Results revealed significant increases in essential amino acids, especially with PGPR + AMF treatment, indicating improved nitrogen assimilation. The contents of cystine, phenylalanine, and tyrosine was also significantly elevated, with AMF and the combined treatment (PGPR + AMF) showing the highest levels. Primary metabolites like amino acids and organic acids (e.g., succinic acid) accumulated significantly, serving as precursors and signaling molecules that stimulate secondary metabolite biosynthesis. Consequently, phenolics, flavonoids, and isoflavones increased markedly following microbial inoculation. These secondary metabolites enhanced antioxidant capacity and plant defense, shown by higher total phenol and tocopherol levels, particularly under combined PGPR + AMF treatment. Improvements in saturated and unsaturated fatty acid profiles further indicate that bioinoculants can elevate the nutritional and industrial quality of soybean seeds. Overall, the buildup of primary metabolites supports the synthesis of antioxidant-rich secondary metabolites, highlighting bioinoculants’ role in enriching seed composition, boosting crop health and resilience, and agro-nutritional value.