Cool-season cover crops have been shown to reduce soil erosion and nutrient discharge from maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] production systems. However, their effects on long-term weed dynamics are not well-understood. We utilized five long-term research trials in Iowa to quantify germinable weed seedbank densities and compositions after 10+ years of cover cropping treatments. All five trials consisted of zero-tillage maize-soybean rotations managed with and without the inclusion of a yearly winter rye (Secale cereal L.) cover crop. Seedbank sampling was conducted in the early spring before crop planting at all locations, with three of the five trials having grown a soybean crop the preceding year, and two a maize crop. Two of the trials (both previously soybean) showed significant and biologically relevant decreases (4,070 and 927 seeds m−2, respectively) in seedbank densities in cover crop treatments compared to controls. In another two trials, one previously maize and one previously soybean, no difference was detected in seedbank densities. In the fifth trial (previously maize), there was a significant, but biologically unimportant increase of 349 seeds m−2. All five trials’ weed communities were dominated by common waterhemp [Amaranthus tuberculatus (Moq.)], and changes in seedbank composition from cover-cropping were driven by changes in this species. Although previous studies have shown that increases in cover crop biomass are strongly correlated with weed suppression, in our study we did not find a relationship between seedbank changes and the mean amount of cover crop biomass produced over a 10-years period (experiment means ranging from 0.5 to 2.0 Mg ha−1 yr−1), the stability of the cover crop biomass production, nor the amount produced going into the previous crop’s growing season. We conclude that long-term use of a winter rye cover crop in a maize-soybean system has the potential to meaningfully reduce the size of weed seedbanks compared to winter fallows. However, identifying the mechanisms by which this occurs requires further research into processes such as seed predation and seed decay in cover cropped systems.