Highly ordered, mesoporous silica thin films with high mass-transport capabilities can be deposited on conductive substrates using the electrochemically assisted self-assembly method. State-of-the-art is, however, limited to films of 50−150 nm thickness, while for thicker layers, the undesired formation of aggregated particles becomes prevalent. In this work, we demonstrate that diffusion layer control using a rotating disk electrode is pivotal to yield aggregate-free films in a wide thickness range (11−2500 nm). The influence of the electrode rotation rate, deposition time/charge, and current as well as temperature on the deposition rate was studied. We show that the film thickness can be inferred from potential transients as the resistivity of the film becomes constant from about 500 nm. Fourier transform infrared spectroscopy, scanning electron microscopy, and transmission electron microscopy were used to determine the morphology and composition of the deposits while a redox probe demonstrated permeability through layers up to 1800 nm thickness. Finally, the coating of micropillars (2 μm diameter, 2 μm spacing, and 50 μm high) and filling of nanotrenches (50 nm wide, 50 nm spacing, and 125 nm deep) with mesoporous silica are shown. The reported results show the first aggregate-f ree thick layers and coating of threedimensional structured electrodes in a single deposition.