A new generation of optically encoded organosilica microspheres, suitable for both solid phase synthesis and multiplexed microsphere-based assays, has recently been described. One of the challenges of producing this type of dual-purpose solid support is that the particles must maintain their morphology as well as their encoding during exposure to the solvents used for solid phase synthesis. In this article, organosilica microspheres are subjected to ammonia treatment methods for enhancing the condensation of the silica matrix and their subsequent resilience toward organic solvents and peptide synthesis reagents is described. The instability of the untreated supports toward organic synthesis reagents was found to be associated with the swelling and permeability of these microspheres in organic solvents. Post-synthesis ammonia treatment resulted in reduced permeability, as demonstrated by dye uptake studies. The treated microspheres exhibited enhanced stability against organic synthesis conditions and were characterized via a variety of techniques including electron microscopy, (29)Si-nuclear magnetic resonance (NMR) and optical microscopy. The ammonia-treated supports were subjected to an Fmoc peptide synthesis procedure and successfully applied in a model microsphere-based flow cytometric immunoassay.