Soy protein isolate (SPI) was hydrolyzed with Flavourzyme® (SHF) or chymotrypsin (SHC). Hydrolysates were sequencially fractionated by ultrafiltration using different membrane pore sizes (50, 10, and 3 kDa). The antioxidant ability of each hydrolysate protein fraction was tested in a liposome oxidizing system and their free radical scavenging activity (FRSA) was evaluated with the DPPH method (diphenylpicrilhydrazine radical). Molecular weight (MW) distribution, solubility, surface hydrophobicity, and amino acid composition of each SPI hydrolysate fraction were measured and their effect on antioxidant and scavenging activities was established by multivariate correlation. The most active ultrafiltrated peptide fractions (P < 0.05), from SHF and SHC, had of MW of <3 kDa (F3 and C3, respectively). These fractions decreased liposome oxidation by 83.2% and 84.5%, respectively, and also showed the highest FRSA (F3: 21.3% and C3: 24.4%). In addition to molecular size, the antioxidant activity and FRSA of soy protein fractions were related to their amino acid composition, especially to an increased content of Phe and a lowered content of Lys. Also, hydrophobicity of ultrafiltrated peptide fractions was an important characteristic (P < 0.001) associated with their ability to trap free radicals. Ultrafiltered peptide fractions with low MW have a high potential to be used as natural alternatives to prevent lipid oxidation in foods.