Soybean seed size and concentrations of protein, oil, sucrose, stachyose, and raffinose are major breeding targets to improve quality. The objectives of this study were to quantify genetic, environment, and genotype-by-environment effects on the stated traits, and to identify and validate quantitative trait loci (QTL) associated with them. Recombinant inbred lines (RILs) derived from two crosses between high-performing food-grade soybeans and imported high-protein edamame (MF1 x OAC Ramsay, and MF1 x DH410) were grown in four Southern Ontario environments. Single nucleotide polymorphism (SNP) markers were generated for RILs using genotyping-by-sequencing. Construction of linkage groups and QTL analyses were done using IciMapping software. Significant genotype-by-environment interactions were found for seed size but no other traits. In total, 94 QTL were discovered underlying the traits of interest, 14 of which were identified in another population or environment. The findings of this study can assist breeders in developing cultivars with improved seed quality.