A method is proposed to control the zeta potential in microchannels using electrically polarisable interfaces in direct contact with the electrolyte. The approach is based on the use of conducting layers exhibiting minimal electrochemical reactions with aqueous electrolytes but a large potential window (typically from −2 V to +2 V) enabling tuning their zeta potential without detrimental faradic reactions. SiC, Al and CNx interfaces were deposited on glass surfaces and then integrated into glass–PDMS–glass devices. The effect of the zeta potential control was monitored by measuring the electro-osmotic flow using a microfluidic Wheatstone Bridge. The experimental results are in good agreement with theoretical predictions based on a one dimensional modeling. The electro-osmotic flow control obtained at high pH values suggests that it should be possible to use such devices as Polarisable Interface Flow-Field Effect Transistors (PI-FFETs) to overcome the difficulties met with conventional metal-isolator-electrolyte systems (MIE-FFETs) for electrokinetic separation applications.