In this work, we present the design, fabrication and characterization of a novel micro-extractor that performs on-line extraction–concentration–detection (ECD) of target molecules flowing in a carrier liquid. The system comprises a primary microchannel containing a flowing aqueous carrier liquid and a secondary organic storage fluid circulating in an adjacent channel. The interfaces between the two immiscible fluids are stabilized by vertical micro-pillars. The system encompasses three functions: (i) extraction of the target molecules from the carrier fluid through the pillar-stabilized interfaces, (ii) concentration of the targets in the secondary organic solvent due to its very low—or zero—velocity and (iii) on-line detection via optical spectrometry. We successively present the analysis of the physics of the system, which has led us to a specific design, then the microfabrication of the chip, and finally we demonstrate the extraction, concentration and detection of lead ions (Pb²⁺) from a water flow.