Non-noble metal catalysts (NNMCs) are regarded as a promising alternative to the costly Pt-based materials required to catalyze the oxygen reduction reaction (ORR) in proton exchange membrane fuel cell (PEMFC) cathodes. However, the large diversity of NNMC synthesis approaches reported in the literature results in materials featuring a wide variety of particle sizes and morphologies, and the effect of these properties on these catalysts’ PEMFC performance remains poorly understood. To shed light on this matter, in this work we studied the physical and electrochemical properties of NNMC layers prepared from materials featuring broadly different aggregate sizes, whereby this property was tuned by ball milling the precursors used in the NNMCs’ synthesis in the absence vs presence of a solvent. This led to two NNMCs featuring similar Fe-speciations and ORR-activities, but with vastly different aggregate sizes of >5 μm vs ≈100 nm, respectively. Following the extensive characterization of catalyst layers (CLs) prepared with these materials via electron microscopy and X-ray tomography, PEMFC tests at different loadings unveiled that the smaller aggregate size and ≈20% higher porosity of the CL prepared from the wet-milled sample resulted in an improvement of its mass transport properties (as well as a ≈2-fold enhancement of its peak power density under H₂/air operation) over the dry-milled material.