Increasing efforts to preserve environmental resources have included the development of more efficient technologies to produce energy from renewable sources such as plant biomass, notably through biofuels and cellulosic residues. The relevance of the soybean industry is due mostly to oil and protein production which, although interdependent, results from coordinated gene expression in primary metabolism. Concerning biomass and biodiesel, a comprehensive analysis of gene regulation associated with cell wall components (as polysaccharides and lignin) and fatty acid metabolism may be very useful for finding new strategies in soybean breeding for the expanding bioenergy industry. Searching the Genosoja transcriptional database for enzymes and proteins directly involved in cell wall, lignin and fatty acid metabolism provides gene expression datasets with frequency distribution and specific regulation that is shared among several cultivars and organs, and also in response to different biotic/abiotic stress treatments. These results may be useful as a starting point to depict the Genosoja database regarding gene expression directly associated with potential applications of soybean biomass and/or residues for bioenergy-producing technologies.