The performance of the current preparative-scale isoelectric trapping systems is limited by the serial arrangement of the separation compartments. A new system has been developed that achieves trapping by recursive electrophoresis in a compartmentalized system (T-RECS). T-RECS features (i) parallel-connected elementary separation heads with independent electrode compartments, feed compartments, and harvest compartments, (ii) orthogonal primary pH gradients and secondary pH gradients, (iii) directionally controlled convective analyte transport along the primary (resolving) pH gradients, and (iv) electrophoretic analyte transport along the secondary (harvesting) pH gradients. The operation of T-RECS has been quantitatively characterized via separation of small molecule ampholytes.