Legumes are able to produce high-protein seeds without nitrogen fertilizer through root symbiosis with nitrogen-fixing rhizobia. Rich in lysine, these proteins are used for human nutrition and animal feed. However, instability of seed protein yield and quality due to environmental fluctuations limits the wide adoption of legumes in Europe. Breeding efforts are needed to optimize and stabilize seed nutritional quality. We have studied the plasticity of protein content and composition of seeds from a collection of 200 ecotypes of Medicago truncatula grown under four controlled conditions (optimal, drought, and winter/spring sowing). A quantitative analysis of one-dimensional protein profiles of these mature seeds was performed and plasticity indices were calculated. Genome-Wide Association Studies (GWAS) were performed from these data and a list of candidate genes under major GWAS hotspots was identified. The selection of candidate regulators for the adaptation of seed protein composition was refined using transcriptomics data from developing seeds. The pea orthologs of these genes were identified for functional studies in this species. The mechanisms that could govern seed protein plasticity to changing environments will be presented, providing new cues towards the improvement of legume seed quality.