•Polysiloxane crown ether column for the analysis of trace perchlorate in vegetables.•Multi-commutated flow-analysis concept with potentiometric detection.•Nanomolar perchlorate determination.•Perchlorate as an environmental contaminant effectively monitored. In this work, an expeditious method based on the multi-commutated flow-analysis concept with potentiometric detection is proposed to perform determinations of the emergent contaminant perchlorate in vegetable matrices down to nanomolar concentration. To accomplish the task, a tubular shaped potentiometric sensor selective to perchlorate ion was constructed with a PVC membrane containing 12mmol/kg of the polyamine bisnaphthalimidopropyl-4,4′-diaminodiphenylmethane and 2-nitrophenyl phenyl ether 68% (w/w) as plasticizer casted on a conductive epoxy resin. Under optimal flow conditions, the sensor responded linearly in the concentration range of 6.3×10−7–1.0×10−3mol/L perchlorate. In order to extend the determinations to lower concentrations (4.6(±1.3)×10−10mol/L perchlorate), a column packed with 70mg of sodium 2,5,8,11,14-pentaoxa-1-silacyclotetradecane-polymer was coupled to the flow-system thus enabling prior pre-concentration of the perchlorate. The proposed procedure provides a simpler alternative for the determination of perchlorate in foods, nowadays only allowed by sophisticated and expensive equipment and laborious methods.