The invention relates to a method for operating an internal combustion engine operable in compression ignition mode, said engine comprising a fuel supply means, a piston in each cylinder causing ignition during compression ignition mode, at least one inlet and one exhaust valve, a control unit that controls the valve timing and fuel quantity, and at least one sensor for measuring an engine operation parameter. The following steps are performed when switching from spark ignition to compression ignition mode: controlling the exhaust and intake valves to perform a negative valve overlap to retain exhaust residual gas, determining a current combustion phasing timing, and correcting the combustion phasing by increasing the retained exhaust residual gas fraction by stepwise control of a combustion related parameter. The invention further relates to an arrangement and a computer readable device for controlling the combustion process.