This study aimed to develop an industrially viable method for rapid detoxification of raw kidney beans (Phaseolus vulgaris L.) while enhancing nutritional properties. Through optimized 5 min water soaking combined with intermittent microwaving (500 W, 5 min), we achieved significant reductions in key antinutrients, namely phytic acid (43–49%), tannins (74–90%), and saponins (59–68%)—all below safety thresholds—concurrently elevating antioxidant capacity (e.g., Ferric Reducing Antioxidant Power: +66–115%) across four colored varieties. Metabolomic analysis of 412 identified metabolites revealed substantial accumulation of key antioxidants including glutathione and quercetin derivatives. Pathway analysis demonstrated dual mechanisms: (1) Detoxification via activated phenylpropanoid biosynthesis degrading tannin precursors and glutathione metabolism reducing phytate; (2) Nutrient enrichment through upregulated phenolic biosynthesis and color-specific flavonoid/betalain pathways. This integrated approach achieves comparable detoxification to 30 min boiling in just 5 min, establishing water-assisted microwave processing as an efficient strategy for industrial-scale production of safer, nutrient-enhanced legumes.