This study was conducted to improve understanding of carbon (C) and nitrogen (N) cycling in alternative agricultural systems. In order to generate information that is directly applicable to farm contexts, the study was conducted in farmer fields. The focus of this study was the soil phase of the C and N cycle, where physical and biological processes transform C and N. However, the design of the study, featuring on-farm research in partnership with farmers, ensured that soil and plant performance factors were integrated with the practical logistics and judgment calls that are exercised by farmers.