Climate change is evident and increases of carbon dioxide concentration (CO2), temperature and extreme weather events are predicted. To predict the effects of such changes on carbon (C) cycling, the processes and mechanisms determining the magnitude of C storage and fluxes must be well understood. The biggest challenge is nowadays to quantify belowground components of the C-cycle. Soil respiration accounts for ∼70% of total annual ecosystem respiration. However, the CO2 flux from soil originates from several sources, such as root respiration, rhizomicrobial respiration, mineralization of litter and mineralization of soil organic matter (SOM). Increasing atmospheric CO2 concentrations will generally increase plant growth, thus C-input to soil. This higher C-input will be accompanied by higher SOM mineralization due to warming. However, mineralization of more stable pools may be affected more by warming compared to mineralization of labile pools. The importance of cropland management is demonstrated in a model scenario. Crop residue incorporation increased C-storage in the soil markedly. However, under the assumption of a higher temperature sensitivity of mineralization of stable C-pools the net-sink of C under recommended management practice is severely reduced. Precise predictions are hampered due to the lack of quantitative, mechanistic knowledge. It is discussed that a more interdisciplinary scientific approach will increase the speed in generating urgently needed understanding of belowground processes of C-cycling.