1. Reducing the deleterious effects of intensive tillage and fertilisation on ecosystem integrity and human health is challenging for sustainable agriculture. The use of cover crops has been advocated as a suitable technique for this purpose, but scientific evidence to support this has been scarce. 2. After four years and a complete rotation; including wheat, maize and green pea as main crops in a ploughing system, we investigated the respective and combined effects of cover crops and nitrogen fertilisation on soil chemical and biological properties using a controlled experiment combining soil chemical analyses, high-throughput sequencing and community level physiological profiles. 3. Cover crops impeded the soil carbon and nitrogen depletion induced by intensive tillage, not only in the topsoil but also within deeper soil horizons, where more specialized bacterial communities established. 4. Cover crops induced a significant shift in soil bacterial community diversity and composition, which was associated with changes in soil chemical features and bacterial metabolic activities along the entire soil profile. 5. Cover crops enhanced soil resilience to nitrogen fertilisation by increasing functional redundancy and complementarity within soil bacterial communities and across soil horizons. 6. Synthesis and applications. In the ploughing systems commonly used for intensive agriculture in Western Europe, the use of cover crops fosters a high functional diversity among soil bacteria and thus can help to achieve a more sustainable agriculture by reducing nitrogen fertilization while maintaining yields.