Weed control is important to improve crop yield in organic farming. In Northern Europe, the use of mechanical weed control restricts the ability to use green manure-cover crops that could be a key source of N supply. In a two-year experiment repeated twice, the objective of this study was to compare the effect of cover crop- and autumn tillage-based systems on N uptake of the succeeding barley crop (Hordeum vulgare L.) and creeping thistle (Cirsium arvense (L.) Scop.). Each autumn, a ¹⁵NO₃^- tracer was applied to the topsoil, and in spring its recovery was measured in the soil, barley and thistle. The effect of cover crops on soil N distribution was significant: 66–85% of the total recovered ¹⁵NO₃^- was in the upper 0.5 m after the cover crop treatments, while after the autumn tillage treatment only 4–8% of the recovered ¹⁵NO₃^- was in this soil layer. The ¹⁵NO₃^- retained by cover crops in the topsoil postponed its availability to the deep-rooted thistle, while making it available to the shallow-rooted spring barley, thus strengthening the barley's ability to compete against thistle. In contrast, following autumn tillage, ¹⁵NO₃^- clearly leached downward; much of it leached below the barley root zone, but remained at depths where it could be taken up by thistle. Cover cropping was found to have a post-harvest control effect on perennial weeds.