To ensure optimum conditions for organic cereal growing, it is important to minimize both compaction and soil inversion depth. The relative effects of using light versus heavier tractors, shallow versus deeper ploughing and on-land versus in-furrow wheel placement during ploughing were investigated in three-year organic rotations dominated by cereals with naturally infested stands of perennial weeds. The second part of the experiments was carried out in continuous barley with transplanted root fragments of Cirsium arvense (L.) Scop. and rhizome pieces of Elymus repens (L.) Gould. Ploughing was performed in spring under favourable weather conditions. Neither tractor weight nor wheel placement influenced decisively the numbers and above-ground biomass of perennial weeds. Depth of ploughing, on the other hand, affected both perennial weed infestation and yield levels consistently. Weed numbers and the total above-ground weed biomass were mostly 50% lower with deep ploughing (25 cm) than with shallow ploughing (15 cm). The greatest advantage of deep ploughing appeared in the control of C. arvense, which in some cases was reduced by more than 90% compared to shallow ploughing. In organic rotations dominated by cereals, therefore, combating of perennial weeds by deep ploughing may be more important than factors such as tractor weight and wheel placement.