This study investigates the effects of timing of fungicide applications alone or in combinations on Fusarium head blight (FHB), seed deoxynivalenol (DON) concentrations, dominant leaf diseases, grain yield, and thousand-kernel weight in winter wheat, spring wheat, and barley in the Atlantic region of Canada. The experiments were conducted for 3 yr (2010–2012), with fungicide treatment as the main factor. Selected commercially available fungicide treatments were applied at two timings: (i) Zadoks growth stage (ZGS) 39: check, propiconazole trifloxystrobin (125 g ha^-1), propiconazole (125 g ha^-1), and pyraclostrobin (100 g ha^-1); and (ii) ZGS 60: check, prothioconazole (200 g ha^-1), prothioconazole tebuconazole (200 g ha^-1), and metaconazole (90 g ha^-1). Results show that a single fungicide application was not sufficient to achieve a high yield with good seed quality. Reduction of visual FHB infection due to fungicide applications did not guarantee a reduction in seed DON concentrations. Fungicide application pyraclostrobin at ZGS 39 and prothioconazole tebuconazole at ZGS 60 was the best treatment, consistently providing the highest crop yield and seed quality, including lowered DON.