Wheat (Triticum aestivum L.) is one of the three most important crops produced worldwide and accounts for 50 percent of the world’s diet. Wheat crops are devastated annually by fungal diseases, with a major one being Fusarium head blight (FHB), caused by Fusarium graminearum. While deployment of resistance QTL has reduced crop losses from FHB, the effect that these QTL have on grain quality and flavor is unknown. The goal of this research is to test if linkage drag associated with pyramided FHB resistance QTL affects agronomic and post-harvest quality of soft red winter wheat (SRWW). In this study, an F₂ population was developed from parents with different QTL combinations, and the QTL status of the 120 F₂  individuals was characterized by genomic predictions. We hypothesized that an increased number of QTL will lower FHB severity but would also negatively affect yield and other traits. To analyze QTL status effects on agronomic traits, twenty F_2:4 lines were planted in a randomized complete block at two locations in Kentucky. Post-harvest grain quality measurements including predicted protein concentrations were measured using near-infrared spectrometry. Flavor profiles were analyzed using roti flatbread from each lines flour and a set of 10 tasters assessed various flavor traits. We found significant differences between deoxynivalenol (DON) content, flavor intensity and likeness, and aroma intensity based on the number of pyramided QTL in the line. Pyramiding QTL led to a significant decrease in DON content. Pyramiding QTL did not consistently affect flavor and aroma in the wheat lines. This research will provide valuable information for breeding decisions regarding disease resistance and maintaining grain quality. A better understanding of FHB resistance in wheat will further development of resistant cultivars while maintaining high quality grain.