Controlling the arrangement and interface of nanoparticles is essential to achieve good transfer of charge, heat, or mechanical load. This is particularly challenging in systems requiring hybrid nanoparticle mixtures such as combinations of organic and inorganic materials. This work presents a process to coat vertically aligned carbon nanotube (CNT) forests with metal oxide nanoparticles using microwave-assisted hydrothermal synthesis. Hydrothermal processes normally damage delicate CNT forests, which is addressed here by a combination of lithographic patterning, transfer printing, and reduction of the synthesis time. This process is applied for the fabrication of structured Li-ion battery (LIB) electrodes where the aligned CNTs provide a straight electron transport path through the electrode and the hydrothermal coating process is used to coat the CNTs with conversion anode materials for LIBs. These nanoparticles are anchored on the surface of the CNTs and batteries fabricated following this process show a fourfold longer cyclability. Finally, this process is used to create thick electrodes (350 µm) with a gravimetric capacity of over 900 mAh g−1. © 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim