An accurate assessment of soil respiration is critical for understanding and predicting ecosystem responses to anthropogenic perturbation such as climate change, pollution, and agriculture. Infra-red gas analyzer (IRGA)-based field measurement is the most widely used technique for assessing soil-respiration flux rates. In this study, respiration rates obtained with two common IRGA systems (LI-COR 8100 and PP Systems EGM-4) were compared across three ecosystem types. Our results showed that both methods were highly comparable in their flux estimates, but the associated methodology used (notably the use or absence of a soil collar) resulted in greater uncertainty in flux rates and a greater degree of intrasite variation. Specifically, the use of collars significantly decreased the flux estimate for both IRGAs compared to the no-collar estimate. The disturbance caused by collar insertion was assumed to be a major factor in causing the differing flux estimates, with root and mycorrhizal severance likely being the main contributor. We conclude that the two IRGAs used in this study can be reliably compared for overall flux estimates but emphasis is needed to validate a common measurement methodology.