The invention relates to a method for the controlled and automatic tensioning of bolts pre-installed in a flange joint between a hub and a main shaft in a nacelle of a wind turbine as well as to a bolt tensioning system for such method. The method comprises arranging a fixture inside the nacelle and mounting a bolt tensioning tool to the fixture which is mounted movable in an axial direction and in a working area perpendicularly hereto. First the flange joint is rotated to position a first set of bolts within the working area of the bolt tensioning tool, and then the bolt tensioning tool is controlled alternately to move the tensioning tool into a position for tensioning a bolt and to tension the bolt, until all bolts of the first set of bolts have been tensioned. The rotation of the flange joint may be controlled by operating a rotation tool operably connected to the main shaft, gearbox, and/or generator.