Micro free flow electrophoresis (μFFE) is a separation technique that continuously separates analyte streams as they travel through an electric field applied perpendicularly to the flow in a microdevice. Application of the technique has been limited by the generation of electrolysis bubbles at the electrodes, which results in unstable flow paths through the device. The current paper introduces the use of surfactants and nonaqueous solvents in the carrier buffer as a means of increasing stability of separated analyte streams. Adding surfactant or nonaqueous solvents lowers the surface tension of the carrier buffer, which we hypothesize promotes the formation of smaller electrolysis bubbles. A 6-fold improvement in the standard deviation of analyte stream position was observed upon addition of 10 mM SDS. Likewise, an approximately 12-fold improvement in stability was observed upon addition of 300 μM Triton X-100. Similar stability improvements were found in carrier buffers containing nonaqueous solvents. An 8-fold improvement in stability was found with a carrier buffer containing 50% methanol and a 6-fold improvement was found with a carrier buffer containing 37.5% acetonitrile. Long term use was demonstrated with a carrier buffer containing 300 μM Triton X-100 in which separated analyte streams remained stable for nearly two hours.