Chlordecone (CHLD), a soil and foodstuff pollutant, as well as an environmentally persistent organochlorine insecticide, was used intensively in banana fields. The chlordecone uptake of three crops was measured for two types of polluted soils: allophanic and non-allophanic. The uptake is lower for allophanic soils even if their chlordecone content is higher than with non-allophanic soils. The fractal structure of the allophane aggregates was characterized at the nanoscale by small angle X-rays scattering, pore size distribution and transmission electron microscopy. We showed that clay microstructures should be an important physico-chemical factor governing the fate of chlordecone in the environment. Allophanic clays result in two counterintuitive findings: higher contaminant trappings yet lower contaminant availability. We propose that this specific, tortuous structure, along with its associated low accessibility, partly explains the low availability of chlordecone confined in allophanic soils. Capsule The fractal and tortuous microstructure of allophane clay favours the chlordecone retention in soils and disfavours the crop uptake. Highlights ? Allophanic soils are highly polluted but less contaminant for cultivated vegetables. ? SAXS and TEM show the fractal structure of allophane aggregates at the nanoscale. ? Allophane aggregates play the role of a labyrinth which fixes and traps chlordecone. ? Allophane physical properties contribute to chlordecone retention in andosols.