Cayenne pepper is an effective natural chipmunk repellent, according to Better Homes and Gardens. The strong scent of the spice repels the chipmunks, keeping them away from bulbs and other food sources when sprinkled over the soil. Rain necessitates a reapplication of the spice for continued benefits.
Chipmunks are attracted to garden bulbs, water, nuts, leaves and berries, notes Better Homes and Gardens. Chipmunks gather these items during the warm summer months, eating them immediately or storing the excess for consumption during the winter. Providing another source of food or using repellents can prevent chipmunks from invading gardens and causing irreversible damage.