We designed, constructed, and tested an automated chamber system for continuously monitoring soil respiration. Our objective was to design a chamber that would permit monitoring of CO 2 efflux rates over long time periods without altering the natural microclimate within the chamber. Furthermore, the design would permit accurate measurements even in a highly fluctuating CO 2 environment. We built a chamber that operates by closing over the soil in response to a control signal and remains closed for a 14‐min period before opening again. Thus, the chamber allows normal drying and wetting of the soil between measurements. An automated switching system was programmed to sequentially open and close chambers in concert with an infrared gas analysis system (IRGA). The IRGA was operated in a differential mode, and equivalent flow rates of reference gas (ambient air) and sample gas (air exiting chamber) were maintained with mass flow controllers. A flexible neoprene lid, stretched tightly over each chamber when closed, provided an airtight seal. This feature and the use of a large mixing bottle (for buffering frequent changes in ambient CO 2 concentration) permitted us to measure soil CO 2 efflux rates even in an environment with highly variable atmospheric CO 2 concentration. Soil respiration rates, measured over a period of several weeks with the automated chambers, were in agreement with traditional point‐in‐time measurements, and the soil microclimate was not affected by the chambers. However, when extrapolated over a period of several weeks the point‐in‐time measurements overestimated CO 2 efflux rates based on continuous measurements with the automated system.