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Abstract Glacial–interglacial cycles constitute large natural variations in Earth’s climate. The Mid-Pleistocene Transition (MPT) marks a shift of the dominant periodicity of these climate cycles from$$\sim 40$$ $\sim 40$to$$\sim 100$$ $\sim 100$ kyr. Recently, it has been suggested that this shift resulted from a gradual increase in the internal period (or equivalently, a decrease in the natural frequency) of the system. As a result, the system would then have locked to ever higher multiples of the external forcing period. We find that the internal period is sensitive to the strength of positive feedbacks in the climate system. Using a carbon cycle model in which feedbacks between calcifier populations and ocean alkalinity mediate atmospheric CO$$_2,$$ ${}_2,$we simulate stepwise periodicity changes similar to the MPT through such a mechanism. Due to the internal dynamics of the system, the periodicity shift occurs up to millions of years after the change in the feedback strength is imposed. This suggests that the cause for the MPT may have occurred a significant time before the observed periodicity shift.