The biocontrol effect of Clonostachys rosea (strains 016 and 1457) on Fusarium graminearum, F. avenaceum, F. verticillioides, F. langsethiae, F. poae, F. sporotrichioides, F. culmorum and Microdochium nivale was evaluated on naturally infected wheat stalks exposed to field conditions for 180 days. Experiments were conducted at two locations in Argentina, Marcos Juarez and Río Cuarto. Antagonists were applied as conidial suspensions at two inoculum levels. Pathogens were quantified by TaqMan real-time qPCR. During the first year at Marcos Juarez, biocontrol was observed in one antagonist treatment for F. graminearum after 90 days (73% reduction) but after 180 days, the pathogen decreased to undetectable levels. During the second year, biocontrol was observed in three antagonist treatments for F. graminearum and F. avenaceum (68·3% and 98·9% DNA reduction, respectively, after 90 days). Fusarium verticillioides was not controlled at Marcos Juarez. At Río Cuarto, biocontrol effects were observed in several treatments at different intervals, with a mean DNA reduction of 88·7% for F. graminearum and F. avenaceum, and 100% reduction for F. verticillioides in two treatments after 180 days. Populations of F. avenaceum and F. verticillioides were stable; meanwhile, F. graminearum population levels varied during the first 90 days, and low levels were observed after 180 days. The other pathogens were not detected. The study showed that wheat stalks were important reservoirs for F. avenaceum and F. verticillioides populations but less favourable for F. graminearum survival. Clonostachys rosea (strain 1457) showed potential to reduce the Fusarium spp. on wheat stalks.