The aim of the current study was to investigate if there are any health effects of long-term consumption of organically grown crops using a rat model. Crops were retrieved over two years from a long-term field trial at three different locations in Denmark, using three different cultivation systems (OA, organic based on livestock manure; OB, organic based on green manure; and C, conventional with mineral fertilizers and pesticides) with two field replicates. The cultivation system had an impact on the nutritional quality, affecting γ-tocopherol, some amino acids, and fatty acid composition. Additionally, the nutritional quality was affected by harvest year and location. However, harvest year and location rather than cultivation system affected the measured health biomarkers. In conclusion, the differences in dietary treatments composed of ingredients from different cultivation systems did not lead to significant differences in the measured health biomarkers, except for a significant difference in plasma IgG levels.