Organic growers must often balance a necessity for mechanical weed control with the importance of maintaining soil health. Despite the wide array of organic cropping systems available to growers striking this balance, the comparative effects of these systems on weed communities are poorly understood. To address this gap, a study was done comparing the weed seed banks and emergent weed communities in four long- term organic cropping systems differing in nutrient inputs and soil disturbance. The results indicated that even minor decreases in nutrient inputs and tillage intensity can increase weed diversity and functional dispersion and act as community assembly filters in the long-term. A second experiment extended the long-term trial by establishing that starter fertilizer does not increase yields in the cover crop-based no- till soybean production used in the low-input cropping systems. Taken together, the studies can guide organic growers seeking to optimize their systems for yield and weed management.