This article demonstrates how to prepare microfabricated columns (microcolumns) for organophosphonate and organosulfur compound separation that rival the performance of commercial capillary columns. Approximately 16,500 theoretical plates were generated with a 3 m long OV-5-coated microcolumn with a 0.25 microm phase thickness using helium as the carrier gas at 20 cm/s. Key to the advance was the development of deactivation procedures appropriate for silicon microcolumns with Pyrex tops. Active sites in a silicon-Pyrex microcolumn cause peak tailing and unwanted adsorption. Experimentally, we found that organosilicon hydride deactivation lowers adsorption activity in microcolumns more than silazane and silane treatments. But without further treatment, the phosphonate peaks continue to tail after the coating process. We found that heat treatment with pinacolyl methylphosphonic acid (PMP) eliminated the phosphonate peak tailing. In contrast, conventional resilylation employing N, O-bis(trimethylsilyl)acetamide, hexamethyldisilazane, and 1-(trimethylsilyl)imidazole does not eliminate peak tailing. Column activity tests show that the PMP treatment also improves the peaks for 2,6-dimethyl aniline, 1-octanol, and 1-decanol implying a decrease in the column's hydrogen bonding sites with the PMP treatment. FT-IR analysis shows that exposure to PMP forms a bond to the stationary phase that deactivates the active sites responsible for organophosphonate peak tailing.