Population and income growth are increasing global food demand at a time when a third of the world’s agricultural soils are degraded and climate variability threatens the sustainability of food production. Intercropping, the practice of growing two or more spatially intermingled crops, often increases yields, but whether such yield increases, their stability and soil fertility can be sustained over time remains unclear. Using four long-term (10–16 years) experiments on soils of differing fertility, we found that grain yields in intercropped systems were on average 22% greater than in matched monocultures and had greater year-to-year stability. Moreover, relative to monocultures, yield benefits of intercropping increased through time, suggesting that intercropping may increase soil fertility via observed increases in soil organic matter, total nitrogen and macro-aggregates when comparing intercropped with monoculture soils. Our results suggest that wider adoption of intercropping could increase both crop production and its long-term sustainability.