A process for preparing fuels, such as diesel fuels or jet fuels, by hydrotreating vegetable oils or fatty acid derivatives that may be applied to existing equipment for treating fossil fuels. The process comprises feeding hydrotreating a combined oxygenate feed stream, such as FAME, and a hydrocarbon feed stream until not more than 86 wt % of the esters in the oxygenate feed stream are converted to hydrocarbons, and optionally further hydrotreating the product stream within at least a second hydrotreatment reaction zone until at least 90 wt % of the esters in the oxygenate feed stream are converted to hydrocarbons, before removing and separating a hydrocarbon stream suitable for use as fuel.