We developed a multiscale model that combines 3D plant architecture with carbon flow in the rhizosphere and soil to understand how dry spells impact carbon and water dynamics, focusing on the activity of the soil microbes. We found that the microbial communities’ characteristics and dry spells’ start dates significantly affect rhizosphere CO₂ emissions and short-term carbon allocation. This model can help understand the effects of climate change on plant growth and rhizosphere carbon dynamics.