A process has been developed for producing diesel boiling range fuel from renewable feedstocks such as plant and animal fats and oils, the process providing for sulfur management. The process involves catalytically treating a renewable feedstock by hydrogenating and deoxygenating to provide a hydrocarbon fraction useful as a diesel boiling range fuel. The hydrocarbon fraction is isomerized to improve cold flow properties. A selective separation such as a hot high pressure hydrogen stripper is used to remove at least the carbon oxides from the first zone effluent before entering the isomerization zone, and to provide liquid recycle to the treating zone at pressure and temperature. A vapor stream is separated from the isomerization effluent and at least carbon dioxide is removed using at least one selective or flexible amine solution absorber. The resulting hydrogen-rich stream is recycled to the deoxygenation reaction zone