Strategies for automatic design of power-optimized 3D-microbattery geometries are here investigated by utilization of the level-set method with structure topology optimization. The methodology is extended from solid mechanics to electrochemical systems, where battery operation is simulated using the Nernst–Planck equation. The calculations are carried out for the 3D-“trench” geometry with LiCoO2 and LiC6 as electrodes, separated with a LiPF6·PEO20 polyethylene oxide polymer electrolyte. With the goal to achieve a maximum uniform electrochemical activity over the electrode surface area, an optimized electrode design is produced by coating the current collectors non-uniformly with active material. This is shown to be an effect of the 3D design of the cell. Evaluation of the resulting optimized cell by simulations of the discharge process demonstrates uniform electrode material utilization and almost uniform current density distribution over the entire electrode–electrolyte interface. Comparisons between optimized and non-optimized geometries showed that the geometry optimization increased the cell performance up to 2.25 times. This effect is mainly achieved by minimizing the internal energy losses caused by non-uniformities in the ionic transport in the battery.