Maryland-grown soybean lines modified for low lipoxygenase-1 (LOX-1) content and a traditional nonmodified cultivar were analyzed for fatty acid composition, total phenolic content (TPC), isoflavone composition, relative DPPH• scavenging capacity (RDSC), and hydroxyl radical scavenging capacity (HOSC). Soybean lines included black, brown, and yellow soybeans. TPC of all soybean lines ranged from 2.84 to 4.74 mg gallic acid equiv (GAE)/g flour. Total isoflavones were between 2.78 and 8.66 μmol/g flour. RDSC of all lines was between 0.48 and 14.62 μmol Trolox equiv (TE)/g flour, and HOSC ranged from 53.57 to 135.52 μmol TE/g flour. Some modified-LOX genotypes demonstrated antioxidant capacity and/or isoflavone content similar to or higher than those of the nonmodified cultivar (P < 0.05). Black soybeans demonstrated higher TPC and RDSC than most yellow soybean lines, although they did not have higher isoflavone content. The results demonstrate that modification of the LOX trait did not necessarily alter the antioxidant capacity or chemical composition of the experimental soybean lines when compared with a nonmodified cultivar. These soybean lines may be studied further for nutraceutical properties and use in functional foods.