A system and method for controlling clock generation. A system includes a processor configured to execute instructions retrieved from memory, and a clock generation system coupled to the processor. The clock generation system is configured to generate a clock signal that the processor applies to execute the instructions. The clock generation system includes a plurality of configuration registers and selection circuitry. Each of the configuration registers includes fields that control a frequency of the clock signal. The selection circuitry selects which of the plurality of configuration registers determines the frequency at a given time.