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Each year, millions of tons of agricultural residues such as wheat straw are produced worldwide. In this paper, we describe ongoing efforts to solve technological, infrastructural, and economic challenges to using this straw for bioenergy and bioproducts. Among these challenges, silica in straw forms a low-melting point eutectic with potassium oxide, causing excessive slagging deposits in boilers. The presence of chlorides causes corrosion beneath the slag deposits on boiler tubes. Silica fouls kilns and fines slow paper machines, limiting the usefulness of straw in linerboard production. Poor resin bonding to the waxy outer cuticle of the straw, poor resin penetration, and high resin consumption due to fines limit the use of straw for straw-thermoplastic composites and for straw particleboard. Poor cellulase penetration limits the use of straw for production of fuels (ethanol) and chemicals. Straw consists of stems, leaves, sheaths, nodes, awns, and chaff. Not all parts of straw are equally valuable. The stems are of higher relative value because they contain much less silica and fines. In contrast, the other plant parts are of relatively lesser value because they are the principle sources of silica and fines. Our approach to reducing silica content is to selectively harvest the straw stems using an in-field physical separation, leaving the remaining components in the field to build soil organic matter and contribute soil nutrients. To address resin issues and cellulase penetration, we are developing distributed windrow system designs employing white rot fungi to upgrade the straw by selectively removing hemicellulose and lignin.