According to the present invention, organic material is converted to biogas through anaerobic digestion and the biogas is purified to yield a combustible fluid feedstock comprising methane. A fuel production facility utilizes or arranges to utilize combustible fluid feedstock to generate renewable hydrogen that is used to hydrogenate crude oil derived hydrocarbons in a process to make liquid transportation or heating fuel. The renewable hydrogen is added to a reactor operated so as to simultaneously desulfurize and hydrogenate crude oil derived hydrocarbons.