Nanoparticle characteristics, including their size, are governed by the reagents employed and the reaction parameters. Here, we systemically vary the catalyst, oxygen content, temperature, and solvent to modify the size and zeta-potential of thiolated organosilica nanoparticles. The particles were synthesized by self-condensation of 3-mercaptopropyltrimethoxysilane in a range of organic solvents in contact with oxygen, with NaOH and other catalysts. The particle size increased with increasing reaction temperature (70 ± 1 nm at 50 °C; 50 ± 1 nm at room temperature) but decreased when air was bubbled through the reaction mixture compared to no bubbling. A significant decrease in the particle size was seen when increasing the dielectric constant of the solvent and when increasing the catalyst concentration; from these, we provide empirical equations that can be used to design particle sizes by manipulating the dielectric constant of the solvent (or cosolvents) or by varying the NaOH catalyst concentration when dimethylsulfoxide is the selected solvent.