The degradation of soil from agricultural land is a major threat to food security and a driver of global changes. Soil conservation systems are thus being promoted and/or adopted worldwide. In this on-farm study conducted in Switzerland, we compared the effect of three cropping systems – conventional with tillage, conventional without tillage (i.e. no-till) and organic farming with tillage – on soil quality. Samples from 60 winter wheat fields belonging to these three systems were analysed for soil carbon concentration, soil aggregate distribution and soil biological properties (microbial carbon and mycorrhizal biomarkers), at three different depths (0–5 cm, 5–20 cm and 20–50 cm). Information about cropping practices was collected through surveys. The main differences in soil properties between systems occurred for the surface layer (0–5 cm depth), with increased soil organic carbon concentration and stock under no-till compared to the conventionally tilled fields. No-till and organic fields showed a higher mean aggregate size and proportion of macroaggregates in the surface layer compared to tilled conventional fields, with a greater amount of carbon in the large macroaggregates. However, large within-system variability was also observed, which tended to override differences between systems. Across systems, clay content, microbial carbon, and the mycorrhizal PFLA biomarkers were the major drivers of soil organic carbon concentration, clay to carbon ratio and carbon accumulation in the large macroaggregate fraction. Aggregation at 0–5 cm was mostly related to tillage depth, while climate variables and especially clay content played a major role for deeper layers. Our results demonstrate that within the constraints set by soil texture and climate, organic agriculture and no-till can contribute to improved soil carbon and aggregation properties. Thus, we advocate for the identification of the main drivers of soil quality.