Abstract. Atmospheric CO2 concentrations changed over ice age cycles due to net exchange fluxes between land, ocean, ocean sediments, atmosphere, and the lithosphere. Marine sediment and ice cores preserved biogeochemical evidence of these carbon transfers, which resulted from sensitivities of the various carbon reservoirs to climate forcing, many of which remain poorly understood. Numerical studies proved the potential of several physical and biogeochemical processes to impact atmospheric CO2 under steady-state glacial conditions. Yet, it is unclear how much they affected carbon cycling during transient changes of repeated glacial cycles, and what role burial and release of sedimentary organic and inorganic carbon and nutrients played. Addressing this uncertainty, we produced a simulation ensemble of various physical and biogeochemical carbon cycle forcings over the repeated glacial inceptions and terminations of the last 780 kyr with the Bern3D Earth system model of intermediate complexity including dynamic marine sediments. This ensemble allows for assessing transient carbon cycle changes due to these different forcings and gaining a process-based understanding of the associated carbon fluxes and isotopic shifts in a continuously perturbed Earth system. We present results of the simulated Earth system dynamics in the non-equilibrium glacial cycles and a comparison with multiple proxy time series. In our simulations the ocean inventory changed by 200–1400 GtC and the atmospheric inventory by 1–150 GtC over the last deglaciation. DIC changes differ by a factor of up to 28 between simulations with and without interactive sediments, while CO2 changes in the atmosphere are at most four times larger when interactive sediments are simulated. Simulations with interactive sediments show no clear correlations between DIC or nutrient concentrations and atmospheric CO2 change, highlighting the likely need for multi-proxy analyses to understand global carbon cycle changes during glacial cycles in practice. Starting transient simulations with an interglacial geologic carbon cycle balance causes isotopic drifts that require several 100 kyr to overcome, and needs to be considered when designing spin-up strategies.