To better understand the factors controlling carbon dioxide (CO2) production and transport in soil, we developed a new method to continuously monitor soil CO2 concentration at multiple depths, by using diffusion chambers. The soil diffusion chambers are constructed from a high‐density polyethylene cylindrical frame enclosed by a micro‐polyvinylidene difluoride flat membrane (PVDF). All chambers are linked to an infrared gas analyser positioned above‐ground through a multi‐port valve system. We set up two experimental sites for long‐term measurements of soil CO2 concentration, soil temperature and soil water content at depths of 0, 10, 20, 40 and 80 cm. The system provides the following advantages : (i) the use of the PVDF combined with the small dimensions of the diffusion chambers allows rapid diffusion of soil gas into the chambers and therefore a short equilibration time of the gas phase with the surrounding soil atmosphere, (ii) the equilibrating closed loop system allows the semi‐continuous measurement of soil profile CO2 concentrations without creating a pressure differential within the chambers, thus reducing gas concentration distortions in the soil, (iii) the small size of the closed diffusion chambers reduces the initial soil disturbance during installation, (iv) it allows sampling in wet, humid soils, including ones that are waterlogged or temporarily saturated, and (v) the chambers do not require removal for maintenance purposes and are inexpensive.