Perennial crops have the potential to accumulate disease over multiple years of continuous growth, though in practice this is not typically observed. As new perennial grain crops are introduced, disease pressure is inevitable. We are developing pipelines to identify, determine advisable primary approaches to reduce disease pressure, and develop tools that can be implemented in breeding programs and in grower fields. Fusarium head blight is one of the most important diseases to control in Kernza®, the first perennial grain crop developed by The Land Institute. Genetic resistance, timing of harvest, and avoiding harvesting lodged crops all reduce the level of Fusarium infection. Future efforts to translate disease forecasting models and evaluate fungicides for use in Kernza offer additional methods of control.