Organic Flour May Contain Fewer Pesticides, but What About Other Contaminants?

By Dr. Chinta SidharthanReviewed by Susha Cheriyedath, M.Sc.Oct 22 2026

A study of 96 French wheat flours examines whether organic labels, shorter supply chains, and milling practices tell consumers enough about what could be lurking in their flour.

Study: Frequent EFSA regulation violation for wheat flours suggests stronger control and regulatory harmonization of production, milling and distribution. Image Credit: CrestBaox08 / Shutterstock

In a recent study published in the journal Npj Science of Food, researchers tested 96 flours from local mills and supermarkets in France's Grand Est region for pesticide residues, mycotoxins, and trace metals, and examined how farming practices, distribution routes, and milling relate to the final product's safety.

Global wheat consumption

Wheat is a staple crop eaten worldwide and a major item in international trade. Pesticides, mycotoxins or fungal toxins, and trace metals can contaminate food through many routes and are potentially harmful with repeated exposure, having been linked to liver, nerve, and immune damage and cancer. To limit risk, governments set maximum residue limits for pesticides and maximum levels for trace metals and mycotoxins. In France, these limits are set under European Union regulations informed by scientific assessments from the European Food Safety Authority (EFSA).

Consumers often choose organic or short-supply-chain foods, believing them safer, but data on combined residue exposure in wheat and how farming and processing affect contaminants remain limited.

The current study

In this study, the researchers collected 96 French wheat flour samples from local mills and supermarkets in the Grand Est region between March and June 2024, including only mills willing to sell to private individuals. The flours were sorted by three characteristics: refinement, defined by ash content (T45, T65, T80, and T150, with T45 the most refined); farming type (organic or conventional); and distribution (short or long supply chains).

The team screened the samples for three contaminant groups. Pesticides, comprising 269 compounds, were extracted and measured by liquid and gas chromatography coupled with tandem mass spectrometry. The mycotoxins included Deoxynivalenol (DON), Ochratoxin A (OTA), Zearalenone (ZEA), HT-2, T-2, and Fumonisin B1 (FB1), which were measured by liquid chromatography with high-resolution mass spectrometry. The researchers also measured 18 trace metals using inductively coupled plasma mass spectrometry.

The researchers compared contaminant concentrations with European regulatory limits, including reference thresholds for raw wheat. Statistical tests compared contaminant concentrations and detection frequencies across flour categories.

The researchers also applied Common Dimensions Independent Component Analysis (ComDim-ICA), an unsupervised multivariate technique, to the combined pesticide, mycotoxin, and trace metal data from 95 samples to identify patterns of variation across the three contaminant groups.

Major findings

The study found that most flours fell below the European thresholds examined, yet the researchers recorded seven exceedances involving permethrin, ochratoxin A, and cadmium. Contaminant levels also differed by farming type, supply chain, and degree of refinement.

Overall, 25 flours (26%) contained at least one quantified pesticide or a pesticide synergist. Three conventional flours from the same mill, sold through short supply chains, exceeded the permethrin reference threshold for raw wheat of 50 micrograms per kilogram, with levels of 70, 297, and 434. Permethrin has not been approved for agricultural pesticide use in the European Union since 2000, and the researchers suggested its presence could indicate relatively recent application rather than historical soil contamination. The synergist piperonyl butoxide was found in 15 conventional flour samples, none exceeding the French threshold discussed in the paper.

Of the mycotoxins that were quantified, DON was detected in 57 samples, while OTA was found in 27. At least one mycotoxin was detected in 73 flours (76%). Three organic flours exceeded the OTA limit of 3 micrograms per kilogram, with the highest value at 13.05 micrograms per kilogram. DON, OTA, and ZEA concentrations were higher in organic flours.

Among organic flours, DON appeared more often in long supply chain products (91.7% versus 33.3%). In conventional flours, pesticide detection was numerically more frequent in short supply chains, while DON concentrations were higher overall in long-chain products.

Of 18 trace metals, 11 were detected in the samples. Cadmium was detected in three samples, with one conventional T80 flour exceeding the cadmium reference threshold for raw wheat of 100 micrograms per kilogram.

Organic flours contained higher concentrations of copper, nickel, zinc, aluminum, iron, manganese, and titanium, whereas conventional products contained more chromium. Less refined flours contained higher levels of copper, iron, manganese, and zinc. Several of these metals are also nutrients, so higher concentrations do not necessarily indicate greater health risks.

The first component of the multivariate analysis explained about 68% of the total variance and was associated mainly with farming type and mycotoxin concentrations. A second component explained roughly 21% of the variance and reflected differences in refinement and trace metal concentrations. These results suggest that an organic label does not guarantee low mycotoxin levels. The findings also showed that regulatory limits for trace metals cover only cadmium and lead in raw cereals.

The authors could not assess storage time or conditions because mills did not supply that information, and they did not measure other contaminants such as polycyclic aromatic hydrocarbons or per- and polyfluoroalkyl substances (PFAS).

Conclusions

Overall, the analysis of 96 wheat flours from France challenged the assumption that organic certification or shorter supply chains necessarily correspond to lower concentrations of every food contaminant. Conventional and organic products showed different contaminant profiles.

Pesticide residues, including permethrin, which is no longer approved for agricultural pesticide use in the EU, appeared mainly in conventional flours, while several mycotoxins and trace metals were higher in organic flours. Certain trace metals were more abundant in less refined products.

The researchers recorded seven exceedances of European reference thresholds, some of which apply to raw wheat rather than flour. The study measured contaminant concentrations rather than dietary exposure or health outcomes, and its regional sampling limits wider generalization.

The findings support closer monitoring of regulatory compliance and further investigation of the roles of farming, storage, milling, and distribution practices in contamination.