Changing vegetation patterns in response to shifting climate over the last glacial period could explain variations in the long-term global carbon cycle, as recorded in trace greenhouse gas (GHG) concentrations in polar ice-core data. However, existing geological records provide only fragments of the vegetation cover history, and the evolution of corresponding carbon stocks and fluxes remains uncertain. Using a comprehensive Earth system model we simulate global transient trajectories of the coupled climate–vegetation–carbon system over 130000 years of the late Quaternary, including intervals with interactive marine biogeochemistry and dynamically coupled ice sheets with iceberg calving. Our aim is to understand how vegetation changes may explain orbital and sub-orbital scale variations in the global carbon budget. According to proxy-based evidence and previous modelling applications, we find that the experiments adequately reproduce known patterns. We focus on how natural land cover transitions and productivity changes contribute to simulated terrestrial emissions of carbon dioxide (CO<sub>2</sub>) and methane (CH<sub>4</sub>). We classify the strength of vegetation changes and locate highly dynamic regions, found closely around monsoon margins, which respond strongly to orbital precession on a multi-millennial timescale, as well as to meltwater discharge in the North Atlantic on sub-orbital timescales. Other regions, however, respond mainly to CO<sub>2</sub> fertilization. During the strong meltwater pulses of the last deglaciation, in a simulation with interactive marine biogeochemistry, land biosphere changes are capable of causing marked atmospheric CO<sub>2</sub> jumps of close to 10 ppmv within several centuries. The simulations together highlight continental regions where interactions between shifting climate and carbon cycle components most likely contributed to GHG variability of the last glacial cycle.