Compression ignition (CI) engines are highly efficient and are therefore often the first choice in application of heavy machinery and heavy duty vehicles. However, diesel engines are known to emit soot and oxides of nitrogen (NOx) emission. Replacing fossil diesel fuel with renewable fuel is one possibility to reduce emissions and to meet legislative requirements. In this experimental work, an oxygenated fuel blend was investigated for soot morphology and results were compared with fossil diesel fuel without oxygenates. Soot was sampled at a medium load case in a light duty single cylinder research engine and samples were analyzed with a transmission electron microscope (TEM). Furthermore, combustion characteristics and particle number (PN) emissions were compared for both fuels. The primary particle diameter (Dp), fringe length (L), fringe separation (S), and tortuosity (T) were also discussed in terms of soot nanostructure. The particle size distribution (PSD) showed a reduction in PN over for the renewable fuel blend compared to diesel. This PN reduction was from 107 to 106 (one order magnitude lower). The maximum Dp from morphological analysis of diesel fuel and renewable fuel was 69.93 and 66.36 nm respectively. Size range of fringe separation (S) was nearly identical for both fuels. Diesel fuel has marginally higher fringe separation, fringe length, and tortuosity. This investigation is valuable for fuel industries which are continuously upgrading renewable and oxygenated fuels to meet stringent emission norms.