Meta-analyses have compared the nutrient content of both organic and non-organic foods. However, the impacts of such variations on human nutritional biomarkers still need to be assessed. In a nested clinical study from the NutriNet-Santé study, we aimed to compare the nutritional status of “organic” and “non-organic” food consumers matched on a propensity score. Based on self-reported organic food consumption assessed through a food frequency questionnaire, 150 low and 150 high organic food consumers were selected with < 10% or > 50% of organic food in their diet respectively (expressed as the proportion of organic food in the whole diet in g/d). Participants were matched using a propensity score derived from sociodemographic, food and health variables. Fasting plasma samples were analyzed using acknowledged laboratory methods for measurements of iron status, magnesium, copper, cadmium, carotenoids, vitamins A and E, and fatty acids. We found significant differences between low and high organic food consumers with similar dietary patterns, with respect to plasma levels of magnesium, fat-soluble micronutrients (α-carotene, β-carotene, lutein and zeaxanthin), fatty acids (linoleic, palmitoleic, γ-linolenic and docosapentanoeic acids), and some fatty acid desaturase indexes. No differences between the two groups were detected for plasma levels of iron, copper, cadmium, lycopene, β–cryptoxanthin, vitamins A and E. If confirmed by other studies, our data suggest that a high consumption of organic foods, compared to very low consumption, modulates, to some extent, the nutritional status of individuals with similar dietary patterns. Further research including prospective cohort studies is needed to evaluate he clinical relevance of such differences.