A two-year research trial was established in Fall 2016 in a corn-soybean rotation field. The cover crops, winter cereal rye (Secale cereal L.) and winter camelina [Camelina sativa (L.) Crantz] were planted soon after each main crop harvest to study the effect of two cover crops used either in both years or in rotation with each other, on corn (Zea mays L.) and soybean (Glycine max. L.) growth and development, root disease and yield in 2017 and 2018. Corn growth and development was better following a cover crop of camelina and had reduced root disease, a lower Pythium population in seedling roots and greater yields compared to corn planted after a cover crop of rye. Cover crop treatments had a positive or no effect on soybean growth and development, root disease and yield. Clade B Pythium species were predominantly detected in corn seedlings, while Pythium Clade F were predominantly detected in soybean seedlings. Moreover, Pythium Clade B populations were greater in corn seedlings planted after a rye cover crop compared to those planted after a cover crop of camelina, while Clade F populations were greater on soybean seedlings planted after a cover crop of camelina compared to those planted after a cover crop of rye. This study demonstrated a cover crop of winter camelina before corn, with or without winter rye in a cover crop rotation system, could be a potential option to mitigate the negative effect of winter cereal rye on corn growth and development.