Soybean is widely used in the food industry because of its high fatty acid and protein content. However, the increased use of pesticides to control pests during cultivation, in addition to being a public health concern, may influence the nutritional quality of soybeans. This study aimed to assess the nutritional quality of soybeans with respect to fatty acid profile and pesticide residue contamination. The levels of fatty acids and pesticides in soybean varieties G196 and G197 were determined by gas chromatography and by the QuEChERS method, respectively. The results showed a significant variation in the quantitative and qualitative fatty acid composition of the two varieties, with 18.03 g/100 g and 4 fatty acids detected for the G196 variety and 21.35 g/100 g and 7 fatty acids for the G197 variety, respectively. In addition, 12 active pesticide compounds were found, and among them, imazalil, quintozene, cyfluthrin and lindane exceeded their maximum limits. The G197 variety had a better nutritional profile compared to G196. The profile of fatty acids and the content of pesticide residues were used as important determinants for soybean utilization in human nutrition.