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Multiple-stage converters are composed of a set of structures with different voltage, current and switching frequency capabilities. In particular, in applications like particle accelerator beam deflection and focusing, the requirement is high-current high-precision current pulses generation. In order to satisfy the specifications of this application, a novel multiple-stage converter topology was proposed and presented in a previous work. However, said proposal should be complemented with a control system to perform the control of each structure, manage its global interconnection and execute the regulation loops. This work describes the implementation of the digital control developed for the proposed converter. Experimental results are presented by applying the proposed control to a prototype.