The novel platinum group metal-free (PGM-free) catalyst for the oxygen reduction reaction (ORR) is synthesized by a modified sacrificial support method (SSM). The catalyst chemical/surface composition is studied by X-ray photoelectron spectroscopy, and the morphology of the material is observed using both HR-SEM and HR-TEM, demonstrating the open-frame, self-supported catalysts. This new catalyst’s electrochemical performance is evaluated by polarization curves and has behaviour comparable to the state-of-the-art PGM-free catalysts. Meso-structure imaging shows pores on the order of 100 nm, the mean size of the individual silica particles in the sacrificial support. For the first time, PGM-free catalyst layer (CL) morphology in a membrane electrode assembly (MEA) is studied in detail by combined nano- and micro X-ray computed tomography (CT) and interpretational modelling. The highly inhomogeneous, high-tortuosity, through-thickness structure of the CL is observed with micro-CT. The nano-CT method for these thick PGM-free electrodes is not sufficient to capture the full through-thickness morphology of these electrodes. Water retention curves suggest water pooling at the MEA components’ interfaces and significant dependence of capilary pressure and saturation on through-thickness location. This study is the first of its kind to identify morphology-dependent transport losses in the thick PGM-free electrodes using scale-bridging between meso-, micro-, and macro.