Climate warming threatens global food security by exacerbating pressures on degraded soils under intensive crop production. Conservation agriculture is promoted as a sustainable solution that improves soil health and sustains crop yields in a changing climate, but these benefits may be affected by long-term warming. Here, we investigate the effects of conservation agriculture compared to conventional agriculture on 17 soil properties, microbial diversity and crop yields, during eight-years’ experimental warming. An overall positive effect of warming on soil health over time under conservation agriculture is characterized by linear increases in soil organic carbon and microbial biomass carbon. Warming-triggered shifts in microbial biomass carbon and fungal diversity (saprogen richness) are directly linked to a 9.3% increase in wheat yields over eight years, but only under conservation agriculture. Overall, conservation agriculture results in an average 21% increase in soil health and supports similar levels of crop production after long-term warming compared to conventional agriculture. Our work provides insights into the potential benefits of conservation agriculture for long-term sustainable food production because improved soil health improves resilience to the effects of climate warming.