We present a simulation workflow for efficient investigations of the interplay between 3D lithium-ion electrode microstructures and electrochemical performance, with emphasis on lithium plating. Our approach addresses several challenges. First, the 3D microstructures of porous electrodes are generated by a parametric stochastic model, in order to significantly reduce the necessity of tomographic imaging. Secondly, we integrate a consistent microscopic, 3D spatially-resolved physical model for the electrochemical behavior of the lithium-ion cells taking lithium plating and stripping into account. This highly non-linear mathematical model is solved numerically on the complex 3D microstructures to compute the transient cell behavior. Due to the complexity of the model and the considerable size of realistic microstructures even a single charging cycle of the battery requires several hours computing time. This renders large scale parameter studies extremely time consuming. Hence, we develop a mathematical model order reduction scheme. We demonstrate how these aspects are integrated into one unified workflow, which is a step towards computer aided engineering for the development of more efficient lithium-ion cells.