A systematic evaluation of continuous flow-counterbalanced capillary electrophoresis for microscale preparative applications is presented. The success of the technique was found to depend on the specific nature of the analyte and background electrolyte and was most heavily influenced by factors such as solution conductivity and rate of buffer depletion. The performance of the technique for the system studied was ultimately limited by contamination arising from changes in analyte mobilities during extended run times. Marked improvements in both purification rate and yield were observed using the zwitterionic buffer 2-(N-cyclohexylamino)ethanesulfonic acid when compared to similar runs carried out using a borate background electrolyte. A quantitative evaluation of the technique was performed for the analytes studied and the performance of the technique has been compared to fraction collection methods. The highest recovery achieved was 5.2% of the fastest migrating component present in the original sample with a resolution of 9 to the adjacent peak and required 100 min under optimized conditions. Recovery could be further increased to 9.0% in 120 min for the same analyte using pressure-ramped flow-counterbalanced capillary electrophoresis.