Organic agriculture aims to build soil quality and provide long-term benefits to people and the environment; however, organic practices may reduce crop yields. This long-term study near Mead, NE was conducted to determine differences in soil fertility and crop yields among conventional and organic cropping systems between 1996 and 2007. The conventional system (CR) consisted of corn (Zea mays L.) or sorghum (Sorghum bicolor (L.) Moench)–soybean (Glycine max (L.) Merr.)–sorghum or corn–soybean, whereas the diversified conventional system (DIR) consisted of corn or sorghum–sorghum or corn–soybean–winter wheat (wheat, Triticum aestivum L.). The animal manure-based organic system (OAM) consisted of soybean–corn or sorghum–soybean–wheat, while the forage-based organic system (OFG) consisted of alfalfa (Medicago sativa L.)–alfalfa–corn or sorghum–wheat. Averaged across sampling years, soil organic matter content (OMC), P, pH, Ca, K, Mg and Zn in the top 15 cm of soil were greatest in the OAM system. However, by 2008 OMC was not different between the two organic systems despite almost two times greater carbon inputs in the OAM system. Corn, sorghum and soybean average annual yields were greatest in either of the two conventional systems (7.65, 6.36 and 2.60 Mg ha−1, respectively), whereas wheat yields were greatest in the OAM system (3.07 Mg ha−1). Relative to the mean of the conventional systems, corn yields were reduced by 13 and 33% in the OAM and OFG systems, respectively. Similarly, sorghum yields in the OAM and OFG systems were reduced by 16 and 27%, respectively. Soybean yields were 20% greater in the conventional systems compared with the OAM system. However, wheat yields were 10% greater in the OAM system compared with the conventional DIR system and 23% greater than yield in the OFG system. Alfalfa in the OFG system yielded an average of 7.41 Mg ha−1 annually. Competitive yields of organic wheat and alfalfa along with the soil fertility benefits associated with animal manure and perennial forage suggest that aspects of the two organic systems be combined to maximize the productivity and sustainability of organic cropping systems.