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Among plant based agricultural products, Nebraska ranks first nationwide in the production of Great Northern beans (GNB), second in proso millet production, and eighth in production of winter wheat. The present research was focused on the effect of processing on nutritive components and in vitro protein digestibility of these crops with the aim of promoting their human consumption. Proso millet based extrudates had physical properties similar to commonly extruded rice but had lower expansion than corn. GNB extrudates had limited expansion and high bulk density mostly due to high fiber and protein content. Extrusion significantly reduced the anti-nutritional components in GNB flour while moderately reducing the essential folate. Extrusion significantly increased the dialyzability of the essential mineral elements Mg, P, K, and Fe in GNB, while significantly reducing dialyzability of the heavy metal Cd. Extrusion also improved the in vitro protein digestibility of GNB flour. In contrast, extrusion had a significant negative impact (almost 50% reduction) on in vitro digestibility of proso millet proteins. Formation of hydrophobic aggregates was the main reason identified for the low digestibility in proso millet proteins. The effect was not specific to extrusion but was observed in all the processing techniques that involved heating above 55 °C. Among various mitigation strategies explored, enzymatic modifications of millet proteins with transglutaminase, heating in low aw solutions, or heating in chaotropic salts (e.g., CaCl2) at high concentration proved to be beneficial in at least partially preventing the low digestibility effect. Further, the results obtained from comparing in vitro digestibility of breads made from legacy and modern wheat cultivars indicated a significant improvement in digestibility of cultivars released after 1931. The old cultivar, Red Chief, and the land race cultivars, Kharkof and Turkey, had significantly lower digestibility than newer rele