One cultivar and five experimental lines of Maryland-grown soybeans with improved fatty acid profiles were investigated for their phytochemical and antioxidant properties. Soybean oils were extracted and analyzed for their fatty acid profiles, tocopherols, and carotenoids. Two of the experimental lines were low in α-linolenic acid and another one was low in both α-linolenic and total saturated fatty acids. The defatted flours were extracted in 50% acetone and 70% ethanol, and estimated for isoflavone compositions, total phenolic contents (TPC), and scavenging capacities against peroxyl (ORAC), hydroxyl (HOSC), and 2,2-diphenyl-1-picryhydrazyl (DPPH) radicals. No difference was observed in tocopherols, carotenoids, TPC, and antioxidant properties between soybeans with reduced α-linolenic and/or saturated fats and the ones with ‘normal’ fatty acid profiles. This study indicates the possibility to produce soybeans with reduced linolenic and/or saturated fat and with desirable levels of health beneficial phytochemicals and antioxidant properties.