New management practices and inputs are always being investigated in order to increase soybean [Glycines max L. (Merr.)] yields. Little information is available regarding the effects of these management practices and inputs on Phomopsis longicolla infection and seed quality. The objective of this study was to evaluate seven commonly used inputs for their impact on P. longicolla infection, seed quality, and yield across the Corn Belt in the United States. A field study was conducted at 17 site-years in Minnesota, Michigan, Iowa, Kentucky, Arkansas, and in Louisiana during 2009 and 2010. The seven inputs were arranged in a non-factorial manner to create nine management systems. The seven inputs were: 1) fungicide/insecticide seed treatment 2) foliar fungicide application at R3 growth stage 3) foliar fungicide application at both R3 and R5 growth stages 4) Bradyrrhizobia seed inoculant 5) soil fertilizer application 6) row spacing (< 76 cm vs. ≥ 76 cm) and 7) seeding rate (357,100 vs. 604,000 seeds ha^-1). Overall, no management system influenced the warm germination or the accelerated aging tests. An application of pyraclostrobin at growth stage R3 reduced P. longicolla infection by 1.9%. Soybean seed yield was increased by 0.32 Mg ha^-1 when planted in narrow rows (< 76 cm) and by 0.26 Mg ha^-1 when a foliar fungicide application was applied at R3. These results indicate that P. longicolla can be reduced and seed yield increased with an application of fungicide at R3. Additionally seed yield can be increased through the use of row spacing less than 76 cm. Our data also suggests that northern states produce higher quality seed and lower P. longicolla infection than do southern states.