These files contain data supporting all results reported in Allen et al., which tested the effects of fertility and tillage intensity gradients on weed communities in long-term organic cropping systems. This study assessed the seed banks and weed communities of a long-term experiment initiated in 2005, which compared four organic systems differing in nutrient inputs and soil disturbance. The high fertility (HF) system received high-rate nutrient applications, low fertility (LF) received low-rate applications, enhanced weed management (EWM) focused on weed control through frequent soil disturbance, and reduced tillage (RT) prioritized soil health with less intense or frequent soil disturbance. Soil samples for greenhouse germination assays were collected at the beginning (2017) and end (2022) of the experiment’s last crop rotation cycle to explore how these four systems influenced seed bank dynamics over time. Weed community biomass was also sampled in each crop. Treatment effects on weed abundance, taxonomic diversity, and community-weighted means and functional dispersion of weed traits were analyzed with generalized mixed effect models. The RT system had the highest weed seed bank taxonomic diversity and EWM had the lowest. RT and LF had higher functional dispersion of traits than HF in the seed bank. Weed seed bank communities in HF and RT were characterized by short, small-seeded, and early germinating weed species. However, seed banks were also labile: differences between systems in seed density and mean trait values were dependent on the crop which preceded seed bank sampling. Likewise, while the traits of emergent weed communities differed in the four system treatments, they depended on an interaction between crop species and their planting year. Results suggest that resource availability and intensity of disturbance act as weed community assembly filters in organic cropping systems. Organic growers seeking to design systems that balance weed management and production goals can use relatively low soil disturbance and nutrient application to increase weed community taxonomic or functional diversity without necessarily increasing weed biomass or seed bank density.