Reductions in sulfur dioxide emissions and the overuse of sulfur-free mineral fertilizers are decreasing soil sulfur and, in turn, threaten the adequate fertilization of most crops. To provide knowledge about legume adaptation to sulfur restriction, we subjected Medicago truncatula, a model legume species, to sulfur deficiency at different developmental stages and compared yield, nutrient allocation and seed traits. This comparative analysis revealed that sulfur deficiency at a mid-vegetative stage decreased yield and altered the allocation of nitrogen and carbon to seeds, leading to reduced levels of major oligosaccharides in mature seeds, which were dramatically affected in their germination. In contrast, during the reproductive period, sulfur deficiency had little influence on yield and nutrient allocation but the seeds germinated slowly and were characterized by low levels of a biotinylated protein, a putative indicator of germination vigor not previously related to sulfur nutrition. Significantly, plants deprived of sulfur at an intermediary stage (flowering) adapted well by remobilizing the nutrients from source organs to seeds, ensuring adequate quantities of carbon and nitrogen in seeds. This efficient remobilization of photosynthates might be explained by vacuolar sulfate efflux to maintain leaf metabolism throughout reproductive growth, as suggested by transcript and metabolite profiling. The seeds from these plants, deprived of sulfur at the floral transition, contained normal levels of major oligosaccharides but their germination was delayed, consistent with low levels of sucrose and glycolytic enzymes needed to restart seed metabolism during imbibition. Overall our findings provide an integrative view of legume response to sulfur deficiency. This article is protected by copyright. All rights reserved.