In temperate regions, reduced tillage is still not broadly accepted in organic farming although the guidelines often recommend the reduction of tillage intensity. During the years 5–7 of a long-term experiment, we studied the effects of the three tillage systems moldboard plowing (MP, soil inversion to 30 cm depth), two-layer plowing (TP, inversion to 15 cm, loosening to 30 cm) and layer cultivation (LC, loosening to 30 cm) on soil nutrients, nutrient content of barley, rye and associated weeds, and yield on a clay loam soil. Crops were cultivated within a five-course crop rotation consisting of green fallow, winter wheat, field peas, winter rye and spring barley; no additional fertilizers were applied. Tillage affected only soil nitrate under barley, which decreased with decreasing tillage intensity. Soil humus, phosphorus (P) and potassium (K) were unaffected by tillage under both crops. Barley shoot nitrogen content was significantly influenced by tillage, with, across years, 38 and 83% higher values under MP than under TP or LC, respectively. Weeds in barley had a higher P and K content at LC than at MP or TP. This resulted, across years, in 73% higher barley yields in MP than in LC. The TP showed a 29% higher barley yield than the LC. Tillage methods had no effect on rye nutrient contents, rye yields or on weeds associated with rye. The significant interaction between tillage and year for rye yield suggests that weather conditions in a given year (e.g., amount of rainfall) can considerably alter the effect of reduced tillage.