Reactors with solid oxide cells (SOC) are highly efficient electrochemical energy converters, which can be used for electricity generation and production of chemical feedstocks. The technology is in an upscaling phase, demanding development of strategies for robust and efficient operation or large SOC reactors and plants. The present state of the technology requires reactors with multiple stacks to achieve the appropriate power. This study aims to establish and apply a simulation framework to investigate process systems containing SOC reactors with multiple stacks focusing especially on the operating behavior of SOC reactors under transient conditions, by observing the performance of all cells in the reactor. For this purpose, a simulation model of the entire SOC reactor consisting of multiple stacks, pipes, manifolds, and thermal insulation was developed. After validation on stack and reactor level, the model was used to investigate the fundamental behavior of the SOC reactors and the individual stacks in various operation modes. Additionally, the influences of local degradation and reactor scaling on the performance were examined. The results show that detailed investigation of the reactors is necessary to ensure operability and to increase efficiency and robustness. Furthermore, the computing performance is sufficient to develop and validate system controls.