Pulse‐labeling with 13CO2 and the subsequent analysis of 13C‐carbon via isotope ratio mass spectrometry (IRMS) have been shown to be an excellent method to investigate the terrestrial carbon cycle. Improving 13CO2 manipulation experiments will facilitate our understanding of carbon cycling processes. A mobile field setup for in situ 13CO2 pulse‐labeling was developed for low vegetation field experiments. Two pulse‐labeling experiments were conducted in a Danish heathland in September 2010 (Exp1) and May 2011 (Exp2). A flow‐through system was developed where labeling chambers were supplied with 13CO2‐enriched air from a gas reservoir. Reservoir and chamber air was sampled over the course of the experiments and analyzed for CO2 concentration and isotopic composition on a GasBench II interfaced with an isotope ratio mass spectrometer. The soil CO2 efflux and the atom% excess in soil respiration were assessed after the 13CO2‐pulse to verify the setup performance. The carbon dioxide concentrations and 13CO2 enrichments were stable during the experiments. The CO2 concentrations conformed to the aimed values, whereas the 13CO2 enrichments were lower than expected. The sources of error for the deviation in observed atom% 13CO2 values are discussed, and a measurement procedure is suggested for samples highly enriched in 13C by using adjusted resistor settings of the mass spectrometer. However, more work has to be done. Enrichment patterns in soil respiration agree with published observations indicating satisfactory performance of the developed system. A mobile flow‐through system suitable for continuous in situ 13CO2 pulse‐labeling was successfully developed that is easily applicable in remote natural ecosystems. Copyright © 2013 John Wiley & Sons, Ltd.