In this study, polyhedral oligomeric silsesquioxane (POSS)-based capillary monoliths with short alkyl chain ligand in the form of butyl (C4) were synthesized via two different polymerization routes, namely UV-initiated free radical copolymerization of methacrylate-derivatized POSS (POSS-MA) with butylmethacrylate (BMA) and UV-initiated thiol-methacrylate copolymerization of POSS-MA with butanethiol (BT). An organosilicon monolith with a pore size distribution lying on both mesoporous and macroporous scales, a lower mean pore size and a higher specific surface area was obtained with UV-initiated thiol-methacrylate polymerization. Both monoliths were then comparatively evaluated for gradient separation of proteins under reversed phase conditions in nano liquid chromatography. The chromatographic performance was defined in terms of peak-resolution and peak capacity. Four carbon (C4) functionalized-poly(POSS-MA) monolith produced by UV-initiated thiol-methacrylate polymerization exhibited better separation performance with higher peak resolutions and peak capacities. Both, the morphological characterization of monoliths and the results of gradient separation of proteins showed that thiol-methacrylate polymerization was more suitable for the synthesis of C4 functionalized organosilicon based stationary phases for reversed-phase protein separation. The monolith prepared by thiol-methacrylate polymerization was also successfully applied for impurity analysis of two important hormones, namely insulin and genotropin. A comparison with a commercial poly(styrene-co-divinylbenzene) monolith documented the good chromatographic performance of the new BT-attached poly(POSS-MA) monolith.