Most battery cells are developed according to a standard design and optimized regarding their electrical properties. However, firstly, there is a demand for an individual cell design adapted to the application. Secondly, additional properties, for example, thermal and mechanical, are decisive for the cell behavior and should be considered in the overall design. Therefore, the present work introduces a model-based development tool for the holistic design of format-flexible battery cells, which are optimized for their future application, allowing for different cell geometries within one battery system. The different approaches and simulation models for the single design steps are presented, and the prediction of the electrochemical, electrical, and thermal behaviors of the cell and whole battery system is described. A key aspect here is the appropriate interconnection of the single models in a way that helps to narrow down the multitude of interacting parameters in a systematic manner and, thus, makes a holistic design possible. In a last step, the functionality of the tool is shown in a case study by means of an e-bike battery pack.