Systems and methods are provided to perform efficient, automatic cyclotron initialization, calibration, and beam adjustment. A process is provided that allows the automation of the initialization of a cyclotron after overnight or maintenance imposed shutdown. In one embodiment, five independent cyclotron system states are defined and the transition between one state to another may be automated, e.g., by the control system of the cyclotron. According to these embodiments, it is thereby possible to achieve beam operation after shutdown with minimal manual input. By applying an automatic procedure, all active devices of the cyclotron (e.g., RF system, extraction deflectors, ion source) are respectively ramped to predefined parameters.