Germination boosted antioxidant capacity and total phenolics in legume seeds, with chickpea showing the largest change isoflavone levels rose over 100-fold, driven by formononetin and biochanin A. Both were isolated and structurally confirmed. HPLC–PDA and LC–ESI–MS profiling found 25 isoflavonoids (including isoflavones, isoflavanones, and pterocarpans), and total isoflavonoids in germinated chickpea were about five times those in germinated soybean. Germinated chickpea is a promising functional food rich in diverse isoflavonoids.