High-performance liquid chromatography is one of the most important analytical tools for the identification and separation of substances. The efficiency of this method is largely determined by the stationary phase of the columns. Although monodisperse mesoporous silica microspheres (MPSM) represent a commonly used material as stationary phase their tailored preparation remains challenging. Here we report on the synthesis of four MPSMs via the hard template method. Silica nanoparticles (SNPs) which form the silica network of the final MPSMs were generated in situ from tetraethyl orthosilicate (TEOS) in the presence of (3-aminopropyl) triethoxysilane (APTES) functionalized p(GMA-co-EDMA) as hard template. Methanol, ethanol, 2-propanol, and 1-butanol were applied as solvents to control the size of the SNPs in the hybrid beads (HB). After calcination, MPSMs with different sizes, morphology and pore properties were obtained and characterized by scanning electron microscopy, nitrogen adsorption and desorption measurements, thermogravimetric analysis, solid state NMR and DRIFT IR spectroscopy. Interestingly, the 29Si NMR spectra of the HBs show T and Q group species which suggests that there is no covalent linkage between the SNPs and the template. The MPSMs were functionalized with trimethoxy (octadecyl) silane and used as stationary phases in reversed-phase chromatography to separate a mixture of eleven different amino acids. The separation characteristics of the MPSMs strongly depend on their morphology and pore properties which are controlled by the solvent during the preparation of the MPSMs. Overall, the separation behavior of the best phases is comparable with those of commercially available columns. The phases even achieve faster separation of the amino acids without loss of quality.