A laboratory and field experiment compared fluxes of CO₂ , CH₄ and N₂O measured with cavity ring-down spectroscopy (CRDS) and gas chromatography (GC). The comparison between CRDS and GC showed that average CO₂ fluxes were significantly higher for CRDS in both the laboratory and field, but the same experimental treatments effects were detected for both techniques. Compared to CRDS, the GC technique was severely limited in detecting CH₄ fluxes in both the laboratory and field. Thus, only 16% of measured GC fluxes were detectable in the laboratory and none in the field whereas CRDS could detect 65% and 97% of the CH₄ fluxes in the laboratory and field. In contrast, N₂O fluxes measured with CRDS and GC were not different for both the laboratory and field. It was observed that a lower proportion of N₂O fluxes could be detected with CRDS (73%) than GC (92%) in the laboratory and similar recovery (65% and 68%) for the field. Thus, the same treatment effects were observed for both CRDS and GC. Furthermore, the comparison between CRDS and GC showed that enclosure times as short as 600 s for our field study site are suitable to estimate the same treatment effects, but not necessarily flux magnitude. We conclude that CRDS and GC can provide the same level of information regarding treatment effects in both laboratory and field experiments for CO₂ and N₂O, but not for CH₄ and it is possible to reduce enclosure time without comprising comparability between the two techniques.