Reduced tillage can improve soil physical quality relative to mouldboard ploughing by lessening soil disturbance, leaving organic matter at the soil surface, and stimulating soil biological activity. In organic farming, continuous ploughing may negate benefits to soil structure and function from increased use of manures and more diverse crop rotations, which are particularly important components of organic farming. The current study examined soil physical quality (i.e., properties and functioning) of a 4-year old reduced tillage system under organic and conventional farming with crop rotations that included root crops. Reduced tillage was compared to conventional mouldboard ploughing (MP) in 2 organic fields at different points of the same crop rotation (Org A and Org B) and 1 conventional field (Conv A). Reduced tillage consisted of non-inversion tillage (NIT) to 18–23 cm depth whereas MP was characterised by annual mouldboard ploughing to 23–25 cm depth. NIT improved soil water retention in Org B but had no effect in Org A. NIT increased soil aggregate stability at 10–20 cm depth compared to MP in all fields, and additionally at 0–10 cm in Conv A. Penetration resistance was higher in NIT in all fields. Furthermore, soil organic matter content was higher in NIT than MP at 0–10 cm depth in all fields and at 10–20 cm in Org B and Conv A. NIT increased carbon stocks in Org B but not in Org A. NIT statistically increased crop yields in spring wheat/faba bean mixture in Org A, and there was no yield penalty from NIT in Org B spring wheat nor Conv A sugar beet. In contrast, field-saturated hydraulic conductivity in all fields in autumn was lower in NIT. Differences in crop (i.e., phase of rotation) and associated organic inputs between Org A and B likely accounted for the differences in effects of tillage system. Overall, the NIT system improved or imposed no penalty on soil physical quality (except field-saturated hydraulic conductivity) and improved or imposed no penalty on crop yields and could therefore be considered as a viable alternative for farmers.