The only serious disease that affects crimson clover is stem rot. The effect of this disease is seen in the early spring and is characterized by the plants dying in patches. The stems rot at the surface of the soil or where they join the crown. The occurrence of continued damp cool weather during early spring favors the development of the disease. Exclusion of clover and other legumes from the rotation for a period of 2 to 5 years is the best control method.

Sandy soils in the southern part of the crimson clover belt are often infested with nematodes. Nematode injury results in a stunting and yellowing of the plants and is most prevalent in the southern part of the region. While the clover-seed chalcid, the pea aphid, and other insects sometimes become numerous in crimson clover, insects do not ordinarily cause appreciable damage.