Effective weed management is critical to the long-term productivity of organic grain cropping systems. The Cornell Organic Cropping Systems Experiment was initiated in 2005 at the Musgrave Research Farm in Aurora, NY to compare four organic cropping systems that differed primarily in intensity of mechanical weed management and soil nutrient inputs. A three-year rotation of corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and spelt (Triticum spelta L.)/red clover (Trifolium pratense L.) was grown in all systems. The four systems were characterized by High Fertility (red clover green manure, composted poultry manure, and commercial organic fertilizer to reach recommended fertility levels), Low Fertility (no fertility inputs other than the red clover and starter fertilizer for corn), Enhanced Weed Management (fertility management as in Low Fertility with additional tillage and cultivation and a higher spelt seeding density), and Reduced Tillage (primarily ridge tillage with different green manure crops). The experiment included two crop rotation entry points, enabling two of the three crops in the rotation to be grown every year. Results from the first two rotation cycles show that, in most cases, weed abundance and diversity increased during the transition to organic production, especially in the Reduced Tillage system. Perennial weeds increased in corn and soybean in the Reduced Tillage system in the second rotation cycle, which contributed to its poor performance relative to the three other systems. Our results suggest that increased soil disturbance, including tillage and cultivation in corn and soybean, plays an important role in reducing weed populations, whereas high fertility levels may exacerbate weed problems. These findings underscore the importance of balancing weed and nutrient management in enabling sustainable organic grain crop production.