Ecological intensification of agriculture calls for ecological mechanisms to replace anthropogenic inputs. Cereal/legume intercropping increases yields due to species complementarities, it produces high protein food and feed, and it reduces the need for artificial N fertilizer because legumes fix N biologically. In addition, intercropping has the potential to suppress plant diseases, but its efficacy for disease suppression in cereal/legume mixtures has not been well characterized quantitatively. Here we conducted meta-analysis to quantify the disease suppressive effect of intercropping cereals with legumes at different levels of N fertilizer. Intercropping reduced disease incidence (measured by the odds ratio of disease occurrence) by 45% on average. This reduction was significant (P < 0.01) for four out of six studied pathogens: yellow rust (Puccinia striiformis f.sp. tritici) and mildew (Blumeria graminis) in wheat (Triticum aestivum), and chocolate spot (Botrytis fabae) and Fusarium wilt (Fusarium oxysporum) in faba bean (Vicia faba). Disease reduction was marginally significant for yellow rust in barley (Puccinia striiformis f.sp. hordei) (P < 0.10) and not significant for bean rust (Uromyces fabae). The reduction in disease incidence was greatest during the early stages of epidemics. N fertilizer strongly increased the incidence of powdery mildew of wheat, but it did not affect the incidence of the other diseases and it did not affect the effectiveness of intercropping as a management strategy for disease control. While nitrogen input increased powdery mildew incidence in both sole and intercropped wheat, the incidence was lower in the intercropped than sole wheat at all levels of N input. The disease suppressive effect of intercropping on wheat powdery mildew or any other disease was not affected by the amount of nitrogen fertilizer. The results show that intercropping has a substantial and consistent effect on disease incidence in cereal/faba bean mixtures across studies, but is not sufficient to provide complete disease control. Intercropping is therefore best used as a component in an integrated approach for managing plant diseases.