Intercropping cover crops have become mandatory in areas at risk of nitrogen leaching to groundwater. These covers include several attractive late-flowering entomophilous species. They can therefore represent crucial floral resources (pollen and nectar) for pollinating insects in early autumn. Pesticides used in previous crops, however, represent a potential risk for pollinators when they are transferred to the intercropping cover plants and their floral resources. We studied the potential transfer of clothianidin (a neonicotinoid insecticide), applied two years earlier in a beet cultivation, from soil to plants and to the floral resources of three common cover species: Phacelia tanacetifolia, Sinapis alba, and Vicia faba. Soils, entire plants, flowers, and nectar were collected from plants grew in greenhouses, and soils and pollen were collected on a treated field. Our results showed that clothianidin was still present in soils (4.5 ng g−1). The residues accumulated in plants (5-15 times higher concentrations than in soils) and were present in pollen of both Vicia faba (0.07 ng g−1) and Sinapis alba (1.7 ng g−1) and in nectar of both Sinapis alba and Phacelia tanacetifolia.