A method for operating a combustion engine is provided. A fuel injector is operated to perform a fuel injection, a sequence of pressure signals of the fuel rail pressure during the fuel injection is sampled and filtered and a total pressure difference between a first sample after a top dead center of the fuel pump and before the fuel injection has started and a chosen second sample after the injection and before a next pumping stroke is determined. A linear pressure slope at the second sample and a leakage pressure difference between the first sample and the second sample based on the linear pressure slope is calculated, leading to calculating an injection pressure difference as the difference between total pressure difference and the leakage pressure difference. With this, a value of a fuel quantity injected as a function of the injection pressure difference can be determined, while leakages are compensated.