Agroecology is defined as the application of ecological concepts and principles to the design and management of sustainable food systems. By viewing cropping systems as agroecosystems, an understanding of the value of the emergent qualities of systems can become a guiding element in research and extension programs. A framework for applying this approach in cropping systems research is proposed. A protocol for researching the conversion to sustainable agriculture involves four levels of investigation. The first focuses on improving the efficiency of conventional farming inputs and practices in ways that reduce their amounts and the environmental impacts of their use. The second focuses on substituting conventional inputs and practices with alternatives that meet broader environmental standards, such as certified organic. Since the problems addressed at these two levels continue to present, a third level is proposed whereby the agroecosystem is redesigned so as to operate on the basis of a new set of ecological processes. At the third level, the emergent qualities of the system itself help prevent problems. Ultimately, though, redesigning food systems will require a focus on reconnecting growers and consumers in a culture of sustainability. This is when the fourth level is applied. How such an approach promotes the conversion to sustainability is discussed.