The invention relates to a microfluidic system including a unit for extracting elements from one liquid phase to at least one other liquid phase, a use of said system for performing said extraction, preferably for gelling polymer capsules coating such elements by cross-linking, and a method for extracting said elements. Said system comprises a substrate in which a network of micro-channels is etched, including a unit (10) for extracting elements (E), including: a depleting micro-channel (11) which carries a first phase (A) to be depleted; at least one enriching channel (12) which carries a second phase (B) to be enriched, said micro-channels meeting at two junctions upstream (Ja) and downstream (Jb) and forming a transfer chamber (13) between said junctions, each junction being such that the micro-channels are axially parallel or form an acute angle on either side of the junction; and a transfer means (14) arranged in the depleting micro-channel for diverting the elements towards the enriching micro-channel. According to the invention, the transfer means includes blocks (14) extending transversely to the axis of the depleting micro-channel, and the extraction unit includes an interface stabilising means (16) arranged downstream from the transfer means between the junctions and including pillars (16) or a surface coating located on an area of the downstream junction facing at least one of the micro-channels.