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Crop producers are challenged to operate profitably, use resources efficiently, meet high standards of quality and protect the environment, while sustaining rural economies and societies. Cropping systems are generally fine-tuned and improved through changes that have small effects which can often be verified only through research. The processes and successes of two farmer research projects were studied. Results of these studies, information from other sources and the authors’ reflections on their own experiences were integrated to develop guidelines for the implementation of farmer research projects for alternative agriculture and multi-functional agro-ecosystems with diverse stakeholders. Surveys were mailed to 118 farmers currently or previously participating in a farmer research project, and to 15 advisors. Responses show that involvement in a farmer research project was profitable, stimulating, enjoyable and worthwhile, despite a substantial time requirement. Tillage and soil fertility research had greater impact on annual farm profit than research on other topics. Farmers and advisors emphasized the importance of the farmers’ roles in identification of research topics, research planning and implementation, and interpretation of the results. Replicated trials conducted over 2 or 3 years were recognized as necessary to adequately verify practices for the corn–soybean rotation of eastern Nebraska, USA. Such trials may need to be complemented with alternative research approaches for improving alternative agriculture and multi-functional agroecosystems where knowledge about some system components is relatively scarce and there is a need to evaluate long-term effects. In conclusion, organized farmer research is an efficient means to cropping system improvement. Guidelines are given for initiation and implementation of farmer research projects.