The most serious disease that affects crimson clover is crown rot. The effect of this disease is seen early in 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. Continued damp, cool weather during winter and early spring favors the development of the disease. This disease can be controlled by not growing clover or other legumes in rotation for 2 to 5 years.

Sandy soils in the southern part of the crimson clover belt are often infested with nematodes. Nematode injury stunts and yellows the plants. While the clover-seed chalcid, the pea aphid, and other insects sometimes become numerous in crimson clover, insects do not ordinarily cause appreciable damage.