Okara, a nutrient-rich soybean byproduct generated in massive volumes (14–20 million tonnes annually), remains primarily underutilized in food systems due to the rapid onset of lipoxygenase-catalyzed off-flavors ("beany," "grassy," "rancid"). This study presents an integrated circular-economy approach to valorize okara into a shelf-stable functional food by overcoming three critical barriers: lipoxygenase inactivation, clean-label emulsification, and in situ vitamin biofortification. A scalable multi-stage thermo-soaking pretreatment (0.1% NaCl soak, 60°C blanching, 90°C heating, and hot-air drying) effectively eliminated sensory off-odors and completely inactivated lipoxygenase, yielding a deodorized okara flour retaining 25.12 ± 0.33% protein (dry basis). Combining this deodorized flour (3% w/w) with soy milk created a novel, clean-label emulsifying system to serve as the structural foundation for the plant-based emulsion. Variants were subsequently subjected to microbial co-fermentation using a vitamin B-producing co-culture of Lactiplantibacillus plantarum (MTCC 25432, 25433, NCDC 772) and Bacillus megaterium NCDC 067. This integrated bioprocessing induced a porous, web-like microstructure that significantly enhanced water-holding capacity and emulsion stability (>98% oil retention under thermal-centrifugal stress). Crucially, in situ microbial biosynthesis biofortified the Honey-Mustard variant with 804.52 ± 65.1 μg/kg of vitamin B₁₂ and 300.13 ± 24.5 μg/kg of vitamin B₂, delivering 469% and 0.32% of the adult recommended dietary allowance, respectively, per 14 g serving. Supported by comprehensive microbiological safety profiling confirming the complete absence of pathogens, this study successfully transforms an abundant industrial waste stream into a high-value, in situ biofortified plant-based emulsion with superior techno-functional and nutritional properties.