Current management of sudden death syndrome (SDS) of soybean, caused by Fusarium virguliforme, focuses on planting resistant varieties and improving soil drainage; however, these measures are not completely effective. A 6-year study evaluated the effects of cropping system diversification on SDS and soybean yield. SDS, root health, yield, and F. virguliforme density in soil were assessed in a naturally infested field trial comparing a 2-year cropping system consisting of a corn-soybean rotation and synthetic fertilizer applications with 3- and 4-year cropping systems consisting of corn-soybean-oat + red clover and corn-soybean-oat +alfalfa-alfalfa rotations, respectively, with both manure and low synthetic fertilizer rates. In 5 of 6 years, SDS incidence and severity were lower and yield higher in the 3- and 4-year systems than in the 2-year system. SDS severity and incidence were up to 17-fold lower in the diversified systems than in the 2-year system. Incidence and severity of SDS explained 45 to 87% of the variation in yield. Plants in the 2-year system generally showed more severe root rot and lower plant weights than plants in the diversified systems. F. virguliforme density in soil was up to fivefold greater in the 2-year system compared with the 4-year system. The processes responsible for the suppression of SDS and yield protection in the diversified cropping systems still need to be determined.