Introduction: Improving soil health while maintaining crop yield is a key challenge for farmers. So far, only a few studies assessed the effects of compost and solid digestate application on soil health and plant yield under practical on‐farm conditions across both organic and conventional cropping systems. Materials and Methods: This study examined 56 arable fields in Switzerland, managed either conventionally (n = 39) or organically (n = 17) by individual farmers. Fields were categorised based on their fertilisation history: standard fertilisation (n = 21), including livestock manure, slurry, and mineral fertilisers (reference), or with additional compost (n = 26) or solid digestate (n = 9) amendments. Soil health was assessed based on eight chemical, biological, and physical soil health indicators. Results: Compost use, but not solid digestate use, was associated with enhanced average soil health ( + 31% over reference fields), driven by increases in basal respiration ( + 45%), cation exchange capacity ( + 42%), fungal richness ( + 18%), and marginally higher soil organic carbon stocks ( + 28%). These differences were consistent across management systems, despite site variability. Clay content and extended periods of crop cover also positively influenced soil health. Wheat yields were 21% lower under organic management but unaffected by compost or digestate use. Conclusion: These findings suggest that using compost alongside practices like extended periods of crop cover can effectively promote soil health while maintaining yields in practical farming scenarios, offering a means to balance multiple sustainability goals simultaneously.