A process has been developed for producing diesel boiling range fuel from renewable feedstocks such as fats and oils from plants and animals where the process provides for sulfur-component 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. A selective separation such as a hot high pressure hydrogen stripper may be used to remove at least the carbon oxides from the first zone effluent and provide a liquid recycle stream at pressure and temperature. A vapor stream is separated from the net process effluent and at least carbon dioxide is removed using at least one selective or flexible amine absorber. The resulting hydrogen-rich stream is recycled to the reaction zone.