In this study, a three-step approach for the immobilization of biomolecules on commercially available filter paper is presented. Photocatalytic coupling of a linker moiety to the paper fibers allows for spatiotemporal control of the immobilization site. An appropriate linker was attached to the biomolecule, allowing catalyst-free, site-specific, and covalent attachment of the biomolecule. Orthogonal linker pairs were evaluated, and five conjugation strategies were identified as providing robust and orthogonal attachment of the desired biomolecule. The suitability of these methods for the generation of complex biofunctionalized papers was demonstrated through premodification of a single sheet of paper with the respective linkers in a spatioselective manner. Application of a mixture of proteins containing the respective linker moieties resulted in successful immobilization of the proteins at the desired sites.