The possibility of immobilizing ex situ-synthesized colloidal bimetallic nanoparticles (NPs) of well-defined characteristics inside hollow core photonic crystal fiber (HC-PCF) microreactors is demonstrated. With the developed method, PtNi clusters remain strongly attached to the fiber core and can be used as active catalysts for the hydrogenation of an azobenzene dye. The study revealed that optical transmission exhibits a size-dependent behavior, i.e., smaller NPs bring in less optical signal loss. Sufficient light transmission was achieved for all particle sizes. Furthermore, with these catalytic PCF microreactors, kinetic data can be obtained with a much lower amount of precious metals compared to a conventional batch reactor, opening a new pathway for in situ catalyst screening.