Agricultural intensification has increased crop yields but resulted in negative consequences for soil health. Here, we investigated the impact of agricultural practices on soil health and crop yields and their interactions across 67 farmer fields in Sweden. To investigate if those factors could explain differences in crop performance between fields, we asked each farmer to select a “good” field with high and/or stable yield and a contrasting “poor” field. At each field, we measured the soil health indicators: plant available water capacity, penetration resistance, wet aggregate stability, bulk density, cation exchange capacity, pH, soil organic matter content (SOM) and basal respiration. Five-year agricultural management information including tillage, crop rotation, application of organic fertilizers and pesticides, and crop yields were obtained from the farmers. Basal respiration was the most sensitive indicator, positively associated with higher crop diversity, more frequent organic fertilizer use, less frequent fungicide use, and lower tillage intensity. Benefits of less intense tillage on soil health was shown by positive relationships between tillage intensity to aggregate stability and SOM. Soil health indicators could not explain differences in yield between “good” and “poor” fields. However, in the “poor” fields, higher yield was associated with more frequent pesticide use, suggesting larger pest, disease and/or weed problems. In the “good” fields, higher crop yield was not directly related to specific practices but associated with higher aggregate stability and SOM and lower bulk density, highlighting the importance of prioritizing practices that enhance soil structure.