The effect of ploughing depth and mechanical soil loading on the performance of pea sole crops, oat sole crops and pea–oat intercrops was investigated in field experiments under organic farming conditions at two sites in Germany in 2009 and 2010. The two ploughing depths were short-term shallow ploughing to a soil depth of 7–10 cm and deep ploughing to 25–30 cm. Wheel loads of 26 and 45 kN, which correspond to typical rear wheel loads of field machinery used during sowing operations, were compared to an uncompacted control. Shallow ploughing resulted in a greater penetration resistance in the 14–28 cm soil layer compared to deep ploughing. An increase in mechanical soil loading intensity increased the bulk density and decreased the air capacity in the 10–15 cm soil layer, whereas the penetration resistance was not affected. The annual weed infestation in pea sole crops was higher after shallow than after deep ploughing at both sites. Pea–oat intercrops compensated for the higher weed infestation after shallow ploughing at one site due to their excellent weed suppressive ability. Dependent on oat productivity, pea–oat intercrops produced comparable or higher grain and protein yields than pea sole crops. Intercropped pea yield components and grain protein yields were significantly lower than those of sole cropped peas. The ploughing depth did not affect pea grain yields in either year and oat yields in 2009. Due to a better emergence, the grain and protein yield of sole and intercropped oats were significantly higher after shallow ploughing in 2010. Mechanical soil loading did not have any effect on the yield performance of pea sole crops, oat sole crops and pea–oat intercrops in 2009. In 2010, mechanical soil loading of 26 kN and 45 kN decreased the pea grain yield by 12.1% and 20.8% respectively, regardless of sole or intercropped. Neither the grain yield nor the grain quality of sole and intercropped oats was affected by the mechanical soil loading in 2010. Grain and crude protein yields of total crop stands decreased with increasing mechanical soil loading after deep ploughing, whereas no significant differences were revealed after shallow ploughing. The present study confirms the positive qualities of pea–oat intercrops with regard to weed suppression and plant performance. Shallow ploughing mitigates the risk of a decrease in crop performance caused by heavy field traffic and provides an alternative to deep ploughing even in low weed competitive organically farmed grain legumes.