Driven primarily by periodic variations in earth’s axis wobble, tilt and orbit eccentricity, our planet experienced massive glacial/interglacial reorganizations of climate and atmospheric CO₂ concentrations during the Pleistocene (2.58 Ma – 11.7 ka). Even after decades of research, the underlying climate response mechanisms to these astronomical forcings have not been fully understood. To elucidate the drivers of Pleistocene glacial cycles it is necessary to first understand how energy gets redistributed in the coupled atmosphere-ocean system on orbital timescales. To this end we conducted an unprecedented transient simulation with the Community Earth System Model version 1.2, which covers the climatic history of the past 3 million years. We identify two major modes of planetary energy transport, which played a crucial role in Pleistocene climate variability: the first obliquity and CO₂-driven mode, is linked to changes in the equator-to-pole temperature gradient; the second mode regulates the inter-hemispheric heat imbalance in unison with the eccentricity-modulated precession cycle. During the Mid-Pleistocene Transition (~ 1 Ma) a pronounced qualitative shift occurs in the planetary energy transport mechanism. After the MPT the second mode synchronizes with the CO₂ forcing, which contributes to an intensification of glacial cycle feedbacks and amplitudes.