In this study, we show the impact of cover crop legacy in soil towards susceptibility of next generation maize to the fungal pathogen Fusarium verticillioides. The use of different plant species as cover crops in organic cropping systems has been shown to provide several ecosystem services. The direct benefits of using leguminous cover crops such as pea or mycorrhizal species such as cereal rye or oats for soil fertility and cash crop yield are well known. However, the impacts of different cover crop species on subsequent cash crop pest suppression is rarely accounted for in agricultural management. Legacy of cover crop species are of importance considering recent findings that plants promoting arbuscular mycorrhizal communities, such as cereal rye and oats as cover crops, can provide increased benefits to successive maize crops against insect pests. In this study, we test whether such benefits might also include resistance against pathogens. We examined progression of rot lesions in ear, stalk and seedling blight by Fusarium verticillioides in maize plants that were grown in soil with a cover crop monoculture history of either winter pea, triticale or radish. This study shows for the first time that soil legacy of mycorrhizal monocot triticale as a cover crop renders maize plants more susceptible to ear rot and seedling blight by Fusarium verticillioides as compared to a soil legacy of radish. This suggests that although soil legacy of radish may be detrimental to management of insects, it is effective in suppressing progression of Fusarium verticillioides in maize. This work demonstrates the significance of cover crop selection to manage fungal pathogens such as Fusarium verticillioides, it further suggests trade-offs in plant resistance to various pests’ taxa at the cover crop species level.