Crop diversification can reduce weed-crop competition and contribute to ecological weed management, but the mechanisms by which crop diversity reduces weed-crop competition and the persistence of those effects are poorly understood. The legacy effects of crop diversity on weed-crop competition were tested after a multi-year field experiment that compared conspecific and heterospecific crop diversity in intercropped annual and perennial systems. In a greenhouse experiment, soil from the field experiment was collected and manipulated to elucidate the effects of soil microbes in determining weed-crop competition. After the final harvest in the field experiment a uniformity trial was conducted to evaluate the effects of crop diversity on weed community structure and compare weed-crop competition. In both cases, crop diversity had minimal effects on weed-crop competition. However, the annual and perennial cropping systems that contextualized the diversity treatments consistently influenced microbial plant-soil feedbacks, crop nutrient uptake, weed communities, and weed-crop competition.