We developed soybean lines with improved amino acid composition (focusing on the sulfur amino acids methionine and cysteine) by suppressing enzymatic steps affecting the supply and turnover of sulfur amino acids. Gene expression analysis during seed development confirmed a reduction in gene levels. Analysis of oil, protein and amino acid content revealed similar oil content between transgenic lines and wild-type, elevated total protein levels (including increased protein-bound cys and met) in transgenic lines, as well as increased free cys and met. In addition, we also developed soybean lines with increased protein content by targeting two proteases implicated in the degradation of protein late in seed development. Analysis of seed from a subsequent generation revealed similar oil content between transgenic lines and wild-type plants. We also stacked the traits by crossing the different lines, resulting in F1 seed for three genotype combinations. In anticipation of the genotyping needs of the stacked lines, we developed markers to identify each trait.