Crop-livestock systems are complex farming systems in which many agricultural practices are combined. Sustainable management of soils in these farming systems requires comprehensive assessment of soil quality and consideration of soil properties and functions in an integrated way. This study evaluated soil quality in a 12-km² watershed that contains intensive crop-livestock farming systems typical of western France and characterized by high animal density and the co-existence of annual crops (cereals and forages, sometimes in rotation with temporary grasslands) and permanent grasslands. Physical (bulk density, aggregate stability), chemical (pH, copper, organic carbon, nitrogen, available phosphorus, C:N) and biological properties (bacterial and fungal abundance and diversity) of the soil were measured in the upper 15 cm of soil at 164 sampling points. Cropping systems at each point were described in detail from farm surveys, which collected data on crop rotations, manure and crop-residue management, fertilizer application and tillage. The variability in soil properties and the impact of cropping systems were quantified at the watershed scale. The percentage of variance of soil properties explained by the cropping system ranged from 6 to 47%, reaching 47%, 36% and 29% for aggregate stability after a fast wetting test, total nitrogen and organic carbon, respectively. Soil biological properties were explained less, but significantly so, by the cropping system as well. Soil properties were combined into a soil quality index. Among variables, crop rotation influenced soil quality the most, much more than manure application. Permanent grasslands and crop rotations with temporary grasslands had significantly higher soil quality indices than annual crops. This approach requires further development to analyze trade-offs among soil properties in crop-livestock systems.