The influence of a platinum:palladium (Pt:Pd)-based diesel oxidation catalyst (DOC) on the engine-out particulate matter (PM) emissions morphology and structure from the combustion of alternative fuels (including alcohol–diesel blends and rapeseed oil methyl ester (RME) biodiesel) was studied. PM size distribution was measured using a scanning mobility particulate spectrometer (SMPS), and the PM morphology and microstructure (including size distribution, fractal geometry, and number of primary particles) was obtained using high-resolution transmission electron microscopy (TEM). It is concluded that the DOC does not modify the size or the microstructural parameters of the primary particulates that make up the soot agglomerates. The PM reduction seen in the DOC is due to the trapping effect, and oxidation of the PM’s volatile components. The DOC performance in reducing gaseous (e.g., carbon monoxide (CO) and unburnt hydrocarbons (HCs)) and PM emissions at low exhaust temperatures was improved from the combustion of alternative fuels due to the reduced level of engine-out pollutants.