Until they become photoautotrophic juvenile plants, seedlings depend upon the reserves stored in seed tissues. These reserves must be mobilized and metabolized, and their breakdown products must be distributed to the different organs of the growing seedling. Here, we investigated the mobilization of soybean (Glycine max) seed reserves during seedling growth by initially constructing a genome-scale stoichiometric model for this important crop plant and then adapting the model to reflect metabolism in the cotyledons and hypocotyl/root axis (HRA). A detailed analysis of seedling growth and alterations in biomass composition was performed over 4 d of postgerminative growth and used to constrain the stoichiometric model. Flux balance analysis revealed marked differences in metabolism between the two organs, together with shifts in primary metabolism occurring during different periods postgermination. In particular, from 48 h onward, cotyledons were characterized by the oxidation of fatty acids to supply carbon for the tricarboxylic acid cycle as well as production of sucrose and glutamate for export to the HRA, while the HRA was characterized by the use of a range of imported amino acids in protein synthesis and catabolic processes. Overall, the use of flux balance modeling provided new insight into well-characterized metabolic processes in an important crop plant due to their analysis within the context of a metabolic network and reinforces the relevance of the application of this technique to the analysis of complex plant metabolic systems.