Soybean (Glycine max L.) seed is a major source of protein, oil, carbohydrates and other nutrients that are important for human and animal nutrition. Producers have considered applying nitrogen (N) fertilizer to soybean crop to maximize seed yield; however, its effect on seed composition is not well understood. The objective of this two-year (2015 and 2016) study was to evaluate the effects of N fertilizer sources and application rates (45, 90, 135 and 179 kg N ha−1) on soybean seed composition on two soil textures (clay and silt-loam) in Mississippi. The three fertilizer sources included in this study were urea with N-(n butyl) thiophosphoric triamide (Urea+NBPT), polymer-coated urea (PCU), and ammonium sulfate (AMS). Nitrogen application at 179 kg ha−1 on clay soil reduced seed protein by 1.05% compared to unfertilized soybeans in 2016. However, N application at 179 kg ha−1 increased oil content by 0.7% on clay soil compared to the unfertilized soybeans only in 2016. Nitrogen applications reduced stachyose content on both soil textures in 2015. The fatty acids showed variable response to N applications. Since, seed quality is not a trait from which growers receive an economic incentive, they are unlikely to adopt this practice for standard soybean production.