In a method and a system for controlling the Variable Turbine Geometry (VTG) of a combustion engine during up-gear shift, the VTG is opened based on a prediction when exhaust gas pressure is stabilized. During up-gear shift the VTG is closed to a closed position (301) to build an exhaust gas pressure and reduce engine speed, and a parameter from which the engine acceleration can be deduced is recorded. The VTG is determined to be opened to an open positioning response to the recorded parameter and a target engine speed of the up-gear shift (303), and the VTG is opened at a time corresponding to said determination to reduce the exhaust gas pressure (305). Hereby the up-gear shift can be made in a short time and at smooth operational conditions.