Porous monolithic stationary phases for capillary electrochromatography have shown great potential due to the ability to tune their properties for tailor-made separations by careful selection of the polymerization parameters. However, the final morphological and chemical properties of the column remain difficult to predict. In order to better understand the effects of the relevant variables on column properties and morphology we have significantly streamlined the preparation procedure and investigated an array of variables (temperature, reaction time, porogenic solvent concentration) on the porosity and retention of the columns. Factorial experimental design was implemented to derive models that were able to describe the polymer porosity and the retention of three PAH’s as a function of starting reagents and conditions. The current study showed that with a factorial design approach, monolith porosity and chromatography can be reliably tuned by adjusting the porogenic solvent concentration, the polymerization time and reaction temperature. Scanning electron microscopy revealed that the polymerization conditions affected the polymer structure and particle size. Synergistic effects not accessible by the “one variable at time” approach were identified between the temperature and polymerization time and temperature and monomer/porogenic solvent ratio through multivariate analysis. The control of the monolith porosity and chromatographic behaviour will allow future efforts to be focused on creating reproducible, tailor-made monolithic columns with targeted chromatographic properties suitable for the separation of peptides and proteins from biological fluids.