Diesel engines are widely utilized as a power source in various applications, such as passenger and commercial vehicles, electricity generation, marine transportation, and construction equipment. Despite several advantages for instance, low operating cost, high durability, and high power-to-weight ratio, diesel engines have the inherent disadvantage of high NOx and soot emissions. In terms of environmental concerns, oxygenated fuels such as biodiesel have been considered as a promising alternative fuel for diesel engines. It is well known that the oxygen content of biodiesel suppresses the formation of soot precursors in diffusion flames. Many researchers are now trying to examine the soot formation with biodiesels. In this chapter, the effect of biodiesel on soot particles in compression ignition engines is discussed. The morphological characteristics of soot particles were analyzed with transmission electron microscope (TEM). The chemical composition was determined by the elemental analysis (EA) and thermogravimetric analysis (TGA). From the previous studies, it emerged that soot particles from biodiesel were composed of smaller primary particles compared to those in case of diesel. The nano-structure analysis of biodiesel soot particles showed that biodiesel origin soot is preferable for oxidation due to its unstable graphene structure. On the other hand, biodiesel soot particles were composed of lesser carbonaceous materials. They contained lower carbon-containing species but higher hydrogen, oxygen, and nitrogen in the soot.