Permafrost regions and boreal wetlands are a known source of atmospheric methane but the magnitude of emissions is unclear. One common way to measure methane emissions in remote polar regions is the static chamber method because of the portability and easy deployment. New multigas analyzers with high frequency concentration measurements reveal patterns and disturbances in chamber methane concentrations over time that call for adjustments in the measurement assumptions, derived from the earlier manual gas sampling methods. In this study, we test whether methodological differences in chamber measurements conceal natural spatial and temporal variations in methane fluxes using an expert survey. A qualitative questionnaire provides information on the variety of approaches for chamber flux measurements, calculation and quality control used by research groups all over the world. By asking experts on greenhouse gas fluxes to process a shared raw data set, we furthermore quantify the difference in methane fluxes resulting from the use of different flux calculation and quality control techniques. Our study shows the potential uncertainties of studies that combine existing flux data sets produced by different research groups as well as the need for a standardized procedure and guidelines for future chamber measurements. This is highly important to reliably quantify methane fluxes all over the world and, especially in Arctic regions where we expect the greatest changes in the near future.