Context: Controlling weeds and reducing the weed seed bank is critical for the success of future crops. The use of cover crops and grazing animals during the transition to organic agriculture can be effective in addressing weed management challenges. Objective: Six objective-based cover crop systems with and without livestock grazing were investigated for their effects on weeds during the organic transition phase at the USDA-ARS laboratory in Mandan, ND. Methods: The study employed a randomized complete block design with a split-plot arrangement and four replicates, with main-plot factors grazed vs. ungrazed, while cover crop systems (soil-building mix, pollinator mix, weed suppression mix, multipurpose cover crop mix, annual crop rotation, or perennial forage biculture) were split-plot factors. Weed seed bank was estimated from soil cores before and after the organic transition and weed density and canopy cover were assessed twice during the growing season each year using the modified Daubenmire method. Results: Cover crop systems affected the weed seedbanks of purslane (Portulaca oleracea L.) and lambsquarters (Chenopodium album L.). Grazing decreased yellow foxtail (Setaria glauca L.) seedbank. Grazing did not affect or total weed plant density; only Setaria glauca weed density was affected; nor did it affect canopy cover. Total weed populations were greater in the multi-purpose and weed suppression mixtures in the second and third years of evaluation. Predominant weed species changed throughout the years, suggesting environmental factors were driving weed growth dynamics. Cover crop systems affected canopy cover. Implications: Outcomes from this study did not support using grazing to control weeds in the transition to organic systems. Study outcomes highlighted the important role of cover crops in controlling weeds during the organic transition phase.