Chlordecone, an organochlorine insecticide, pollutes soils and contaminates crops and water resources and is biomagnified by food chains. As chlordecone is partly trapped in the soil, one possible alternative to decontamination may be to increase its containment in the soil, thereby reducing its diffusion into the environment. Containing the pesticide in the soil could be achieved by adding compost because the pollutant has an affinity for organic matter. We hypothesized that adding compost would also change soil porosity, as well as transport and containment of the pesticide. We measured the pore features and studied the nanoscale structure to assess the effect of adding compost on soil microstructure. We simulated changes in the transport properties (hydraulic conductivity and diffusion) associated with changes in porosity. During compost incubation, the clay microstructure collapsed due to capillary stresses. Simulated data showed that the hydraulic conductivity and diffusion coefficient were reduced by 95 and 70% in the clay microstructure, respectively. Reduced transport properties affected pesticide mobility and thus helped reduce its transfer from the soil to water and to the crop. We propose that the containment effect is due not only to the high affinity of chlordecone for soil organic matter but also to a trapping mechanism in the soil porosity.