Quantifying carbon dioxide (CO2) fluxes between soil and atmosphere is key in understanding net ecosystem C exchange and biogeochemical C cycling in plant-soil systems. In ecosystems with low primary production and sparse vegetation, for example, dry lands or subpolar regions where C fluxes are small, measurement sensitivity is key—even so when measurements are combined with isotopic labeling. Here, we present a simplified gas sampling system developed to facilitate sampling and measurement of low soil CO2 fluxes as well as in situ 13CO2 labeling in the same setup. The capacity of the system was tested in a set of feature tests along with gas measurements of dryland soil-biocrust systems. The system's sensitivity to capture minor changes in CO2 concentration was confirmed in respiration and photosynthesis measurements of soil-biocrust systems, where fluxes down to 0.1 μmol CO2 m−2 s−1 were quantified. A balloon, implemented to counterbalance underpressure build-up during gas withdrawal, mitigated 72% of pressure differences at sampling. The overall system volume was reduced to a minimum to limit contamination caused by residual air, and the design enabled one-step flushing and evacuation of system compartments and gas sample bags, successfully ruling out cross-contamination between samples. Ultimately, this system offers a flexible and accessible solution for CO2 measurements that can be applied not only on arid soils with low biological activity and turnover rates, but also on plant-soil systems. The modifications enabled larger, and thereby more representative, sample volumes to be collected while limiting incubation, contamination, and pressure effects on the intact soil system.