Plant–soil interactions are recognized to play a crucial role in the ecosystem response to climate change. We developed a facility to disentangle the complex interactions behind the plant–soil C feedback mechanisms. The MICE (‘Multi-Isotope labelling in a Controlled Environment’) facility consists of two climate chambers with independent control of the atmospheric conditions (light, CO2, temperature, humidity) and the soil environment (temperature, moisture). Each chamber holds 15 plant–soil systems with hermetical separation of the shared above ground (shoots) from the individual belowground compartments (roots, rhizosphere, soil). Stable isotopes (e.g. ¹³C, ¹⁵N, ²H, ¹⁸O) can be added to either compartment and traced within the whole system. The soil CO2 efflux rate is monitored, and plant material, leached soil water and gas samples are taken frequently. The facility is a powerful tool to improve our mechanistic understanding of plant–soil interactions that drive the C cycle feedback to climate change.