Corn (Zea mays L.)–soybean [Glycine max (L.) Merr.] cropping systems of the Midwest have led to increased selection pressure on diseases caused by Fusarium pathogens. A field experiment was conducted from 2010 to 2012 near Arlington, WI, to identify interactions among disease management practices (crop rotation, host resistance, and fungicide use) that increase corn, soybean, and wheat (Triticum aestivum L.) yields. For corn grain, significant interactions were primarily driven by crop rotation. Highest corn yields across all 3 yr were observed in the corn–soybean–wheat (CSW) rotation (13.55 Mg ha−1). Corn silage yield was influenced by cultivar rotation, with highest yields displayed by the Fusarium‐susceptible rotations (susceptible followed by susceptible followed by susceptible [SSS] and susceptible followed by susceptible followed by resistant [SSR]). Soybean yields were influenced by interactions involving crop rotation and cultivar rotation. Highest soybean yields were found for crop rotations containing wheat and ranged from 5.1 to 8.4% higher than the corn alternated annually with soybean (CS) rotation. The Fusarium‐resistant (resistant followed by resistant followed by resistant [RRR]) cultivar rotation (4.14 Mg ha−1) yielded 3.0% better than the next highest rotation (SSR). Crop rotation, cultivar selection, and fungicide use were all key drivers for wheat yield. Highest yields on average were observed in the CSW rotation (5.62 Mg ha−1). The Fusarium head blight (FHB)–susceptible cultivar (5.50 Mg ha−1) yielded significantly higher compared to the resistant cultivar (4.89 Mg ha−1), and fungicide use increased yield in the susceptible cultivar 7.2% (5.31 to 5.69 Mg ha−1) but not for the resistant cultivar. Although interactions were not consistent for all three crops, our results suggest growers should begin with combining a high‐yield‐potential cultivar, regardless of its susceptibility or resistance to Fusarium pathogens, in a CSW crop rotation to maximize yield potential when managing Fusarium‐related diseases.