A three-phase microchip was developed for the rapid and efficient small-scale purification of alkaloids from plant extracts. As part of the development of such a three-phase microchip, first a two-phase microchip with two channels (3.2 cm and 9.3 cm) was used to study the extraction efficiency of strychnine nitrate and strychnine at various flow rates. Strychnine was extracted from a basic aqueous phase to a chloroform phase (extraction) or strychnine was extracted from a chloroform phase into an acidic aqueous phase (back extraction). Subsequently, the "simultaneous extraction and back extraction" of strychnine was carried out in a three-phase microchip. The experimental extraction rate and yield were compared with model data. At a residence time of 25 sec, 79.5% of strychnine was extracted into the acidic aqueous phase using the three-phase microchip. In general, a good correlation was found between experimental results and model data for both two- and three-phase extractions. Finally, the three-phase microchip was employed in the purification of alkaloids (strychnine and brucine) from Strychnos seed extracts. © The Royal Society of Chemistry 2009.