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.