Farmer-researcher partnerships are needed to ensure soil and crop management practices are productive, environmentally safe, economically sound, and socially acceptable. We developed a farmer-researcher partnership to compare nutrient, labor, energy, and economic budgets for two “conventional” 40-acre fields where a 2-yr corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotation is used with those for two adjacent fields where a 5-yr corn, soybean, corn, oat (Avena sativa L.), and hay rotation is used. Conventional fields received commercial fertilizer and herbicides. Alternative fields received no herbicides and a mixture of animal manure plus municipal sewage sludge as the primary nutrient source. A 10- yr nutrient budget suggests that N2 fixation would have to provide at least 53% of the N removed by soybean grain to prevent depletion of soil organic matter or other soil N sources from conventional fields. By assuming similar amounts of N fixation in the alternative fields, we show that 962 lb N/acre, 244 lb P/acre, and 844 lb K/acre were applied (or fixed) in excess of crop removal. Soil-test P, K, and organic matter changes reflect these applications. More fieldwork hours per acre per year were required to handle manure, avoid using herbicides, and harvest hay than to use conventional practices. Energy budgets were dependent on whether nutrients in the manure plus municipal sludge were considered as (i) an input cost for the crop, or (ii) a disposal cost that should be charged against an animal enterprise. Economic budgets were dependent on assumptions made regarding how to account for management costs. Overall, developing farmer-researcher partnerships was an effective method for evaluating alternative farming systems.