Soybeans (Glycine max (L.) Merill) are popularly known as a healthy food in many Asian countries and are mostly consumed as soymilk, tofu, and fermented products such as miso, temph, and sufu. The objective of this study was to determine the variation and composition of phenolic compounds and isoflavone contents in soybean seeds [Glycine max (L.) Merill] and sprouts [Kongnamul] grown under dark conditions (producing yellow soybean sprouts) and in green and yellow boxes (producing green soybean sprouts). In seven soybean cultivars, the total phenolic content ranged from 6.67 μg−1 in Pureunkong to 72.33 μg−1 in Poongsannamulkong. The average total phenolic content in the green soybean sprouts (48.33 μg−1) was higher than in the yellow soybean sprouts (29.75 μg−1). The total phenolic content in the yellow soybean sprouts varied from 9.88 μg−1 to 47.71 μg−1, and the total phenolic content in the green soybean sprouts varied from 29.21 μg−1 to 79.70 μg−1. Only four phenolic compounds, p-hydroxybenzoic acid, salicylic acid, p-coumaric acid, and ferulic acid, were detected in all soybean cultivars. Syringic acid was not detected in yellow soybean sprouts, and myricetin was only detected in yellow soybean sprouts (4.65 μg−1) from the Pureunkong cultivar grown under dark conditions. The total isoflavone content in soybean seeds ranged from 2.1 μg−1 in Sowonkong to 33.0 μg−1 in Pureunkong, and the mean total isoflavones was 10.61 μg−1. Green soybean sprouts had higher average total isoflavones (1389.4 μg−1) than yellow soybean sprouts (559.2 μg−1), and the total isoflavone content was highest in the Pureunkong yellow soybean sprouts (756.3 μg−1) and the Sowonkong green soybean sprouts (2791.6 μg−1). In soybean sprouts, the higher the (malonyl)-daidzin or (malonyl)-genistein content, the higher the total isoflavone level. Our study suggests that producing soybean sprouts enriched in isoflavones under coloured-light sources is feasible.