Bipolar plates (BPPs) are key components in vanadium redox flow batteries (VRFBs) as they contribute to a major part of cell stack costs. The main functions of a BPP are to prevent mixing between the electrolytes, conduct electrons, and provide mechanical support to the electrodes in a VRFB stack. Conductive carbon-polymer composites have been considered promising candidates for BPP due to their cost-effectiveness, lightweight, and good processability. During the production of such composite BPPs, different manufacturing imperfections such as delamination, trapped gases, cracks, inclusions, and voids can occur. In addition to these defects, the dispersion of filler particles can also affect the electrical conductivity. Therefore, in the current study, we investigated the influence of conductive filler type on the inner structure of the BPPs and correlated it with electrical conductivity. The BPPs analyzed in this work consisted of 80 wt% conductive filler: crystalline graphite and/or carbon black and 20 wt% polymeric binder. From through-plane conductivity measurements, we observed that replacing a fraction of graphite with carbon black enhances electrical conductivity. Since the constituents of these BPPs, viz., graphite, carbon black, and polymer differ in terms of their crystallinity, morphology, and density, we make use of a combination of synchrotron-based computed tomography (CT) techniques, i.e., X-ray diffraction (XRD) CT and phase-contrast nano-imaging to obtain information about the inner structure of these composites, which in turn could be correlated to their electrical conductivity. This work has demonstrated that the application of XRD-CT and phase-contrast imaging can be successfully employed for the characterization of carbon-polymer composites, which usually suffer from poor contrast due to low absorption coefficients.