A process to remove organic sulfur from organic compounds and organic carbonaceous fuel substrates containing sulfur compounds having sulfur-carbon bonds is disclosed. The steps of the process include oxidizing the sulfur species to the sulfone and/or sulfoxide form, and reacting the sulfone and/or sulfoxide form in an aqueous media of the reacting step including a hydride transfer reducing agent. In a particular embodiment, the reducing agent is sodium formate, the oxidizing agent is a microorganism as exemplified by Rhodococcus species ATCC 55309 or Rhodococcus species ATCC 55310 or combinations thereof.