A method for producing middle distillates from a feedstock produced by Fischer-Tropsch synthesis and containing oxygenated compounds, including: a) a step of bringing the feedstock into contact with a hydrotreating catalyst allowing the methanation of the CO and CO2 contained in the feedstock or originating from the decomposition of the oxygenated compounds present in the feedstock, b) a step of hydroisomerization/hydrocracking of at least a part of the liquid and gaseous effluent originating from step a), in the presence of a hydroisomerization/hydrocracking catalyst, c) a step of gas/liquid separation of the effluent originating from step b) into a gaseous fraction comprising predominantly hydrogen and a hydroisomerized/hydrocracked liquid fraction, d) a step of fractionation of the liquid fraction separated in step c) to obtain at least one fraction of middle distillate, in which the hydrogen in step a) is obtained from the gaseous fraction separated in step c).