The geologic history of atmospheric CO2 concentration (CAtm) is relevant to studies of paleoclimate, paleobiology, and elemental cycling at the Earth's surface. Here we present a model that represents processes controlling the concentration, stable carbon isotope composition, and vertical distribution of organic matter and CO2 within soils. In the model we include a volumetric scaling term necessary to calculate the soil pore CO2 concentration and δ13CO2 from soil respiration rate per unit area, which has been omitted in previous work. Our model provides several new insights into the commonly used method for estimating paleo-CAtm based on the δ13C of paleosol carbonates. We show that because refractory, microbially processed organic matter is increasingly abundant toward the base of the soil, isotope effects associated with organic matter decay can potentially lead to significant offset between the δ13C of soil-respired CO2 (δϕ) and that of soil organic matter at depth. The magnitude of this effect depends on the production and decay characteristics of the individual soil, and can lead to substantial underestimation of paleo-CAtm if organic matter preserved in subsurface paleosol horizons is used to approximate δϕ. Paleo-CAtm reconstruction will be more accurate if surface-layer fossil organic matter is used as a proxy for δϕ. In this case, however, there is a small (200--300 ppm), consistent, positive bias in CAtm estimates resulting from the decay of 13C-enriched organic matter deep within the soil. Re-examination of earlier studies using the soil carbonate approach to estimate CAtm identifies examples where each bias may be present.