A microfluidic double channel device is employed to study reactions at flowing liquid–liquid junctions in contact with a boron-doped diamond (BDD) working electrode. The rectangular flow cell is calibrated for both single-phase liquid flow and biphasic liquid–liquid flow for the case of (i) the immiscible N-octyl-2-pyrrolidone (NOP)–aqueous electrolyte system and (ii) the immiscible acetonitrile–aqueous electrolyte system. The influence of flow speed and liquid viscosity on the position of the phase boundary and mass transport-controlled limiting currents are examined. In contrast to the NOP–aqueous electrolyte case, the acetonitrile–aqueous electrolyte system is shown to behave close to ideal without ‘undercutting’ of the organic phase under the aqueous phase. The limiting current for three-phase boundary reactions is only weakly dependent on flow rate but directly proportional to the concentration and the diffusion coefficient in the organic phase. Acetonitrile as a commonly employed synthetic solvent is shown here to allow effective three-phase boundary processes to occur due to a lower viscosity enabling faster diffusion. N-butylferrocene is shown to be oxidised at the acetonitrile–aqueous electrolyte interface about 12 times faster when compared with the same process at the NOP–aqueous electrolyte interface. Conditions suitable for clean two-phase electrosynthetic processes without intentionally added supporting electrolyte in the organic phase are proposed.