High charge and discharge rates are desired properties for Li-ion batteries of both macro- and micro-scale (i.e. a footprint area of < 1mm2). Under these conditions, a rise of the cell temperature can take place, leading to performance limitations and safety issues. Investigations of thermal effects in battery cells provide possible explanations of the limiting factors of cell performance and can suggest improvements. We present here extensive simulations with a fully coupled 3D thermal-electrochemical model of 3D microbatteries (3D-MBs) using Finite Element Methodology (FEM). 3D-MB architectures comprising pillar shaped, plate shaped and concentric electrode arrangements are simulated, using LiCoO2 and graphite as electrodes and solid polymer electrolytes with LiTFSI salt. Sensitivity analysis of the electrolyte diffusion coefficient, depending on the C-rate, is used to benchmark the performance of these 3D-MB cells. FEM simulations of the 3D-MB during operation provide a complete 3D time-dependent description of the thermal behavior of the cells. Temperature gradients in the cell highlight critical regions which are likely causing performance bottlenecks and safety hazards. The simulations clearly demonstrate that the highest heat sources appear near the regions with most active charge transfer processes, thereby providing insights for optimization of the cell geometry in terms of both performance and safety.