Silica monoliths were fabricated inside fused-silica capillaries. Then the monolithic columns were coated with membrane-like zirconia. The zirconia-coated silica monoliths exhibited different EOF behavior comparing with that of bare silica monoliths. The magnitude and direction could be manipulated by changing the running buffers. Due to the amphoteric characteristic of zirconia, the silica monoliths with zirconia surface facilitate the separation of basic compounds. Aromatic amines and alkaloids were separated without obvious peak tailing. The zirconia surface was easily modified with octadecylphosphonic acid for the separation of neutral compounds. Column efficiency as high as 90,000 and 80,000m−1 was obtained for beberine and naphthalene, respectively. Furthermore, the zirconia coating increased the stability of the monolithic columns. Even after being exposed to severe condition, there was no apparently efficiency decrease for the test samples.