This study presents a simple synthetic approach for the in situ preparation of monodisperse hybrid Janus microspheres (HJM) having organic and inorganic parts in a PDMS-based microfluidic device. Based on the mechanism of shear-force-driven break-off, merged droplets of two photocurable oligomer solutions having distinctive properties are generated into an immiscible continuous phase. Functionalized perfluoropolyether (PFPE) as the organic phase and hydrolytic allylhydridopolycarbosilane (AHPCS) as the inorganic phase are used for the generation in aqueous medium of HJM with well-defined morphology and high monodispersity (average diameter of 162 µm and a 3.5% coefficient of variation). The size and shape of the HJM is controlled by varying the flow rate of the disperse and continuous phases. The HJM have two distinctive regions: a hydrophobic hemisphere (PFPE) having a smooth surface and a relatively hydrophilic region (AHPCS) with a rough, porous surface. In addition, pyrolysis and subsequent oxidation of these HJM convert them into SiC-based ceramic hemispheres through the removal of the organic portion and etching off the silica shell. The selective incorporation of magnetic nanoparticles into the inorganic part shows the feasibility of the forced assembly of HJM in an applied magnetic field.