Sulfur (S) and nitrogen (N) are elements naturally found in petroleum-based fuels. S- and N-based compounds in liquid fuels are associated with a series of health and environmental issues. Thus, legislation has become stricter worldwide regarding their content and related emissions. Traditional treatment systems (namely hydrodesulfurization and hydrodenitrogenation) fail to achieve the desired levels of S and N contents in fuels without compromising combustion parameters. Thus, oxidative treatments (oxidative desulfurization–ODS, and oxidative denitrogenation-ODN) are emerging as alternatives to producing ultra-low-sulfur and nitrogen fuels. This paper presents a thorough review of ODS and ODN processes applying carbon-based materials, either in hybrid forms or as catalysts on their own. Focus is brought to the role of the carbonaceous structure in oxidative treatments. Furthermore, a special section related to the use of amphiphilic carbon-based catalysts, which have some advantages related to a closer interaction with the oily and aqueous phases, is discussed.