Bacterial canker is a serious disease of sweet cherry that limits orchard life and tree productivity. New York tree fruit growers ranked the need for research on bacterial canker in the top ten. Currently, copper sprays are used to manage the disease, however, the effectiveness of copper sprays in protecting pruning cuts is unknown. Leaving a 15-cm-long pruning stub to manage the lethal canker phase of the disease has shown promise. The occurrence of copper-resistant bacteria and negative impacts of copper on soils underscore the need for research. We studied the effectiveness of spring copper sprays and the pruning stub in preventing canker infection. Neither copper nor pruning stubs prevented infection of inoculated and uninoculated pruning cuts. Six training systems were assessed and ranked in order of increasing bacterial canker incidence as follows: Perpendicular V, Zahn Vertical Axis, Marchant, Vogel Slender Spindle, Modified Central Leader, and Spanish Bush. Five cultivars in each training system ranked in order of increasing bacterial canker incidence as follows: Sweetheart, Lapins, Tehranivee, Hedelfingen, and Regina . Our results suggest that applying copper sprays may not improve control of the canker phase of this disease. The pruning stubs appeared to impact the progression of the disease by distancing infections from the main trunk. The Perpendicular V and Zahn Vertical Axis orchard training systems showed the lowest vulnerability to canker infections. Further research is needed to determine the pruning strategy’s effectiveness on long term management of the disease.