A first aspect of present invention is related to a method for controlling the extraction of ion beam pulses produced by a synchrocyclotron according to an irradiation plan. The synchrocyclotron comprises electrodes configured to be placed in a magnetic field, wherein an alternating voltage is applied between the electrodes, and wherein the frequency of the alternating voltage is modulated in a cyclic manner. The method comprises the steps of starting an acceleration cycle of the synchrocyclotron (12), generating a reference signal (38) when the modulated frequency reaches a predefined value (42), communicating the time, at which the reference signal (38) is generated, to the one or more beam control elements (20, 22), assessing one or more status parameters of the one or more beam control elements (20, 22), wherein the assessment is synchronised with the generation of the reference signal (38), cancelling or proceeding with the extraction of the beam pulse depending on the results of the assessment. A second aspect of the present invention is related to an ion beam extraction system configured to perform the method according to the first aspect of the present invention.