The through-plane gas permeability and morphology of PEFC gas diffusion media (GDM) is investigated for different microporous layer (MPL) ink homogenisation techniques (bath sonication and magnetic stirring) for low- (Vulcan XC-72R) and high (Ketjenblack EC-300J)-surface-area carbon powders. The MPL composition is held constant at 80 wt.% carbon powder and 20 wt.% PTFE for a carbon loading of 1.0 mg cm−2. The MPL ink homogenisation time is held constant at two hours for both techniques and increased by one hour for bath sonication to compare with previous investigations. The results show that the through-plane gas permeability of the GDM is approximately doubled using magnetic stirring when compared with bath sonication for MPLs composed of Vulcan XC-72R, with a negligible change in surface morphology between the structures produced from either homogenisation technique. The variation in through-plane gas permeability is almost negligible for MPLs composed of Ketjenblack EC-300J compared with Vulcan XC-72R; however, MPL surface morphology changes considerably with bath sonication, producing smoother, less cracked surfaces compared to the large cracks produced via magnetic stirring for a large-surface-area carbon powder. An MPL ink sonication time of three hours results in a percentage reduction in through-plane gas permeability from the GDL substrate permeability by ~72% for Ketjenblack EC-300J compared to ~47% for two hours.