The transition period to certified organic production can present a significant weed management challenge for growers. Organic certification requires that prohibited fertilizers and pesticides must not have been used for 36 mo before harvest of the first organic crop. Understanding how organic management practices and initial weed seed-bank densities affect weed population dynamics during the transition period may improve weed management efficacy and adoption of organic practices. We examined how tillage systems (full or reduced) and cover crop species planted during the first transition year (rye or a mixture of timothy and red clover) affect the seedling densities of three common annual weed species, common lambsquarters, velvetleaf, and foxtail spp., during the 3-yr transition period. Weed seeds were applied in a one-time pulse at the beginning of the study at three densities, low, medium, and high (60, 460, and 2,100 seeds m−2, respectively), and cumulative seedling densities of each species were assessed annually. Treatment factors had variable and species-specific effects on weed seedling densities. In general, the full-tillage system, with an initial cover crop of timothy and red clover, resulted in the lowest density of weed seedlings following seed-bank augmentation. There was little consistent association between the initial densities of applied weed seeds in the weed seed bank at the start of the transition and weed seedling densities at the end of the transition period. This suggests that when multiple crop and weed cultural management practices are employed during the organic transition period, initial failures in weed management may not necessarily lead to persistent and intractable annual weed species management problems following organic certification.