X-ray dynamic tomographic microscopy offers new opportunities in the volumetric investigation of dynamic processes. Due to data complexity and their sheer amount, extraction of comprehensive quantitative information remains challenging due to the intensive manual interaction required. Particularly for dynamic investigations, these intensive manual requirements significantly extend the total data post-processing time, limiting possible dynamic analysis realistically to a few samples and time steps, hindering full exploitation of the new capabilities offered at dedicated time-resolved X-ray tomographic stations. In this paper, a fully automatized iterative tomographic reconstruction pipeline (rSIRT-PWC-DIFF) designed to reconstruct and segment dynamic processes within a static matrix is presented. The proposed algorithm includes automatic dynamic feature separation through difference sinograms, a virtual sinogram step for interior tomography datasets, time-regularization extended to small sub-regions for increased robustness and an automatic stopping criterion. We demonstrate the advantages of our approach on dynamic fuel cell data, for which the current data post-processing pipeline heavily relies on manual labor. The proposed approach reduces the post-processing time by at least a factor of 4 on limited computational resources. Full independence from manual interaction additionally allows straightforward up-scaling to efficiently process larger data, extensively boosting the possibilities in future dynamic X-ray tomographic investigations.