We describe the assembly of silica nanoparticles into superstructures with controlled shape and size. The individual nanoparticles are chemically linked to each other via silica bridges, thus providing high mechanical stability to the assembly. Key to control the size and shape of the assemblies is the confinement of the nanoparticles in highly monodisperse microdroplets that are produced in a microfluidic chip. Exploiting the high surface-to-volume ratio of the assemblies, we show an enzymatic reaction on them. To control the position of the assemblies in a microfluidic environment, we embed superparamagnetic nanoparticles into them, which allows us to move the assemblies with a simple hand magnet.