Marginal areas with acid soil conditions are widely available in Indonesia. However, the low pH and nutrients associated with acid soil may limit the productivity of soybean. Therefore, soybean varieties tolerant to acid soil is needed as well as information on the nutrient contents and bioactive components to support their utilization for foods. This study was performed to identify the protein, fat, fatty acid, and isoflavone contents of 20 soybean promising lines tolerant to acid soil. The results showed that three lines contained high protein (≥45% dry weight = dw), namely Tgm/Anj-888, Tgm/Anj-862 and Tgm/Anj-858. The fat contents ranged from 16.85 to 21.20% dw and showed a negative correlation with the protein content (r = -0.64). On average, soybean fat consisted of 9.42% palmitic acid (C16:0), 2.77% stearic acid (C18:0), 43.93% oleic acid (C18:1), 38.53% linoleic acid (C18:2), and 5.35% linolenic acid (C18:3). Ten isoflavones were identified with malonylgenistin as the major component (29.49%), followed by malonyldaidzin (19.04%) and glycitin (16.70%). Tgm/Anj-995 line showed the highest total of isoflavones (2,130.2 μg/g dw), followed by Tgm/Anj-784 and Tgm/Anj-832 (1,719.9 μg and 1,710.0 μg/g dw, respectively). This nutritional information would be useful for the breeder to release new soybean varieties tolerant to acid soil as supportive data to their agronomic characters.