Abstract <p>Qualitative investigation of the mechanisms of greenhouse carbon dioxide transformation in the soil–plant–atmosphere system requires specialized instrumentation capable of constructing ecosystem models, monitoring ongoing transformations, and processing the resulting data. To expand the methodology for studying carbon dioxide fluxes, we developed an installation for investigating CO₂ transformation mechanisms in the soil–plant–atmosphere system, which simulates and maintains autonomous plant viability while simultaneously recording and displaying the diurnal dynamics of CO₂ concentration within a fully closed system. For a more detailed assessment of the directionality of carbon dioxide transformation, the installation provides complete isolation of the plant’s aerial and subterranean parts. During the installation testing, we used a Paulownia seedling with a mass of 7.47 g, whose developed roots were immersed in river sand enriched with a nitroammophos solution (NPK 16 : 16 : 16). Over a period of 30 days, the iMK LoRa measurement complex recorded CO₂ uptake and release in two zones of the installation at 5-minute intervals. The model experiment demonstrated that the plant can continue growth and development in the absence of an external carbon dioxide source, and biomass formation (+111.8%) occurs via root carbon nutrition. In this case, soil carbon partially (76.4%) enters the atmosphere through plant respiration and is reabsorbed during the light phase, thus sustaining a “small carbon cycle.” The remaining portion of soil carbon (23.6%) contributes directly to biomass formation, bypassing transformation through the leaf apparatus. The proposed installation enables the identification of specific carbon nutrition regimes for various crops, supporting the selection of techniques and agronomic practices for biomass regulation.</p>