The history of organic agriculture includes traditional agriculturalists who first farmed without the use of synthetic fertilizers and pesticides. Sir Albert Howard (1873–1947), however, is considered the foremost pioneer of codified organic methods, along with Rudolf Steiner (1861-1925) and Jerome Rodale (1898-1971)–all citing soil quality and the integration of livestock in mimicry of natural systems as key elements of organic agriculture. Following the inception of the California Certified Organic Farmers organic certification agency in 1973, organic agriculture underwent a rapid expansion, with numerous agencies serving U.S. farmers, leading to a unifying, federal, USDA National Organic Program rule in 2002, and an estimated 1.7 million hectares under organic production by 2005. Increasing demand for crop and livestock products for the $15 billion organic industry has led to greater requests for research-based organic information at land-grant universities. Participation of the farming community in organic agricultural research activities is essential for the development of applicable strategies that take into account their priorities, practices and perspectives. In the Long-Term Agroecological Research program at Iowa State University, we have involved organic farmers in the design and analysis, and in complementary on–farm trials examining soil processes in the organic transition and beyond certification. Organic corn yields over a 9–yr period were 9.8 Mg/ha compared to 10 Mg/ha in the conventional system; organic tofu soybeans yielded the same as conventional at 3 Mg/ha. Average production costs in the conventional C-S rotation were found to be $119/ha higher than the average organic rotation (C-S-O-A) costs during organic transition. The 2–yr average organic returns ($282/ha) were similar to the conventional C-S returns, but even greater in the third year ($840/ha), following certification. Soil quality remains high in the organic systems, with more SOC, TN, and biologically-active OM, greater structural stability, and lower soil acidity.