As soil–atmosphere fluxes of greenhouse gases are characterized by high temporal fluctuations, frequent measurements in the range of hours to days need to be deployed, resulting in high analytical costs. We have therefore developed a new low-cost system that combines high-frequency automated sampling with low-frequency chemical analysis. The System for Inert Gas Monitoring by Accumulation (SIGMA) is suited particularly for stand-alone observations in remote locations. The SIGMA is connected to an automated chamber with headspace sampling several times per day. Air samples are aggregated in sampling bags, which reduces the number of subsequent laboratory analyses and allows calculation of average flux rates over extended sampling periods. The SIGMA was tested under field conditions and compared with a conventional autochamber system, where flux rates were measured several times per day. Sample air fillings of the SIGMA sampling bags varied less than 5% between bags and diverged <1 to 6% of the pre-set values, justifying the assumption about proportional mixing of chamber headspace samples. When the SIGMA and conventional autochambers were compared simultaneously over the same patch of grassland in Denmark, the estimates agreed within ±12% in the assessment of average N2O fluxes. When deployed to discrete autochambers situated a few metres apart and under various environmental conditions in Denmark and the UK, we found no consistent difference between the two measuring systems. For a N-fertilized cropland in Denmark the SIGMA N2O and CO2 fluxes were 28 and 23% less, respectively than those recorded with the conventional autochamber, while for a N-fertilized grassland in the UK the SIGMA N2O flux was 47% more than that recorded with the conventional autochamber and 6% less than that recorded with a manual chamber system. Such differences are within the range of natural spatial variability in trace gas fluxes for these ecosystems and indicate the potential for further application of the SIGMA approach as a cost-effective technique to estimate long-term trace gas fluxes.