The effects of N dose and stage of ripeness on Fe, Co, Cr, Ni, Se and N concentration and incidence of fungal diseases were measured in winter wheat grain from conventional (CONV) and organic (ORG) systems on neighbouring areas of a 10-year-old manure-based farm. Principal components analysis (PCA) of the data showed that year had the greatest influence on the results, but that cropping system affected N, Ni, Fe and Se content and incidence of diseases. Attack by Dreschlera tritici-repentis was highest in ORG and attack by Stagonospora nodorum in CONV. Increasing stage of maturity increased incidence of fungal disease and Fe content. Analysis of variance and MANOVA showed that wheat yield was affected by weather (precipitation and temperature), cropping system and N dose. The 10% lower yield in ORG than CONV was explained by a lower amount of plant available N at the same N dose. Nitrogen, Fe, Ni, Se and Co contents in grain were affected by year, while dry matter content was significantly lower in ORG than in CONV. The MANOVA identified correlations between Co and Fe, Ni and Se. Incidence of fungal diseases was foremost affected by weather, stage of ripeness and N dose. Organic cropping increased Fe and Se uptake and decreased S. nodorum attack, but increased attack by D. tritici-repentis.