Context Little is known about the long-term contribution of cover crops to weed management in tillage- and herbicide-based systems. Research questions Do cover crops mainly filter weed species capable of setting seeds during the fallow period? Can cover crop biomass productivity explain differences in weed suppression among cover crop species? Does reduced weed seedbank density translate into lower weed biomass and higher crop productivity? Methods Soil samples (0–15 cm) were collected in 2018 after cover crop termination and used in a greenhouse seedling emergence assay to assess the topsoil weed seedbank capable of germinating 25 years after the beginning of a split-plot experiment on tillage systems (conventional vs. reduced) and cover crops (bare soil control, Brassica juncea (brown mustard), and Vicia villosa (hairy vetch)). Total density and density of the 10 most abundant weed species in the topsoil seedbank were related to observations of weed species visual soil cover, total weed biomass, cover crop biomass, and cash crop grain yield made during the six years which preceded the weed seedbank assessment. Weed seedling density was also used to compute community weighted mean of germination and flowering period. Results In comparison with the bare soil control, hairy vetch suppressed total weed seedling density by 40%, whereas brown mustard showed no effect. In comparison with the bare soil control, hairy vetch suppressed weed seedling density of Cerastium glomeratum (−87%), Veronica persica (−86%), Capsella bursa-pastoris (−57%) and Poa annua (−42%), whereas brown mustard only suppressed C. bursa-pastoris (−65%) and V. persica (−49%). The suppressive effect of hairy vetch on these four species translated into a significant reduction of community weighted mean of autumn/winter germination period and March to July flowering period. The contrasted suppressive effect of brown mustard and hairy vetch on weed seedling density of these four species was related to contrasted competitive interactions during the four previous cover crop seasons. However, differences in weed suppression between hairy vetch and brown mustard could not be fully explained by differences in biomass productivity. Management intensity (e.g. herbicides and tillage) potentially smoothed out differences in weed suppression between cover crop treatments because no effect of cover crops were observed on total weed biomass or gain yield of the subsequent crops over the 2012–2017 period. Conclusion Cover crops contribute little to weed management in herbicide and tillage-based cropping systems. Implication The weed suppressive effect of cover crops should be further explored in cropping systems which minimise herbicide use and tillage intensity.