A microbiological method of desulfurization (MDS) of hydrocarbon fuels such as coal, coal tar and petroleum uses an aqueous microbial biocatalytic agent which is not significantly reproducing but is still capable of oxidizing inorganic sulfur compounds and/or of selectively cleaving sulfur-carbon bonds in organic compounds, thereby removing sulfur with insignificant losses in fuel value. Microorganisms are selected according to the type of fuel sulfur present and the environment in which the desulfurizing process is to take place. One embodiment allows droplets of highly concentrated cell-water suspensions to pass from the top surface of the fuel through to the bottom, desulfurizing along the way and removing the sulfur products of the process as well. This MDS method can be used during hydrocarbon fuel production, storage, transport, and/or processing conditions, thereby also providing an added benefit in corrosion protection of the vessels used for these functions.