We report the microfluidic chip-based assembly of colloidal silanol-functionalized silica nanoparticles using monodisperse water-in-oil droplets as templates. The nanoparticles are linked via silica bridges, thereby forming superstructures that range from doublets to porous spherical or rod-like micro-objects. Adding magnetite nanoparticles to the colloid generates micro-objects that can be magnetically manipulated. We functionalized such magnetic porous assemblies with horseradish peroxidase and demonstrate the catalytic binding of fluorescent dye-labeled tyramide over the complete effective surface of the superstructure. Such nanoparticle assemblies permit easy manipulation and recovery after a heterogeneous catalytic process while providing a large surface similar to that of the individual nanoparticles.