This article describes the preparation of spherical Janus particles by microcontact printing. A set of three different polymer beads (diameter ca. 170 μm), each bearing different functional groups at their surface, are used to covalently attach distinct functional molecules exclusively on opposing poles of the beads. The covalent modification of the beads involves three different types of click chemistry: epoxide ring opening (ERO), copper catalysed azide–alkyne cycloaddition (CuAAC) and thiol–yne addition (TYA). These reactions are compared with regard to their advantages and disadvantages in the context of “sandwich” microcontact chemistry. The success of surface modification of the beads is verified by fluorescence microscopy and 3D-time of flight secondary ion mass spectrometry measurements and is further supported by reference experiments on planar surfaces bearing the same surface functionality and analysed by X-ray photoelectron spectroscopy, secondary ion mass spectrometry, atomic force microscopy and fluorescence microscopy. Furthermore we demonstrate that sandwich microcontact printing can also be performed on smaller polymer beads with a diameter of ca. 5 μm. The broad scope of surface chemistry in combination with the simple experimental setup makes this method attractive to a wide range of material science applications, since it combines orthogonality of surface functionalization with high pattern fidelity.