A process in which the paraffinic effluent derived from a Fischer-Tropsch synthesis unit is separated to obtain a heavy C5+ fraction, said heavy fraction then being hydrogenated in the presence of a hydrogenation catalyst at a temperature in the range 80° C to 200° C, at a total pressure in the range 0.5 to 6 MPa, at an hourly space velocity in the range 1 to 10 h-1, and at a hydrogen flow rate corresponding to a hydrogen/hydrocarbons volume ratio in the range 5 to 80 NI/I/h, the liquid hydrogenated effluent then being brought into contact with a hydroisomerization/hydrocracking catalyst, with no prior separation step, the hydroisomerized/hydrocracked effluent then being distilled to obtain middle distillates and possibly oil bases.