Natural systems agriculture is based on an understanding that natural systems are self-sustaining due to regulatory mechanisms and processes that help to ensure the long-term maintenance of the ecosystem. An agroecosystem modeled after nature should encompass greater stability and biodiversity at all levels of organization than an agroecosystem based on conventional agricultural practices. The main objective of this study was to determine whether agroecosystems modeled after nature exhibit advantages over conventional agroecosystems. Five treatments were examined: winter wheat (Triticum aestivum L.) monoculture, alfalfa (Medicago sativa L.) monoculture, strip-cropped alfalfa and wheat, and two alfalfa–wheat intercrops (one no-till and one conservation-till). Indicators of ecosystem function studied included primary productivity, soil fertility, plant nitrogen (N) concentration, and abundances of arthropod pests and predators. No fertilizers or pesticides were used prior to or during this investigation. Monoculture, strip-crop and conservation-till treatments produced significantly higher yields than no-till intercropped alfalfa and wheat. Although yields from the no-till intercrop were low, wheat protein values were comparable to other treatments. Soil N concentrations tended to be high in treatments containing alfalfa. Insect pests preferred alfalfa and were, therefore, often more abundant in treatments containing high percentages of alfalfa, as were predators such as spiders. Researching alternatives to monoculture agroecosystems, such as the intercrop systems in this study, may provide us insight into a true natural systems agriculture.