A method, system and processor for increasing the instruction throughput in a processor executing longer latency instructions within the instruction pipeline. Logic associated with specific stages of the execution pipeline, responsible for executing the particular type of instructions, determines when at least a threshold number of the particular-type instructions is scheduled to be executed. The logic then automatically changes an execution cycle frequency of the specific pipeline stages from a first cycle frequency to a second, pre-established higher cycle frequency, which enables more efficient execution and higher execution throughput of the particular-type instructions. The cycle frequency of only the one or more functional stages are switched to the higher cycle frequency independent of the cycle frequency of the other functional stages in the processor pipeline. The logic also automatically switches the execution cycle frequency of the specific pipeline stages back from the second, higher cycle frequency to the first cycle frequency, when the number of scheduled first-type instructions has completed execution.