We have carried out an inter-comparison between EddyUH and EddyPro®, two public software packages for post-field processing of eddy covariance data. Datasets including carbon dioxide, methane and water vapour fluxes measured over two months at a wetland in Southern Finland and carbon dioxide and water vapour fluxes measured over three months at an urban site in Helsinki, were processed and analysed. The purpose was to estimate the flux uncertainty due to the use of different software packages and to evaluate the most critical processing steps, determining the largest deviations in the calculated fluxes. Turbulent fluxes calculated with a reference combination of processing steps were in good agreement, the systematic difference between the two software packages being up to 2% and 6.7% for half-hour and cumulative sum values, respectively. The raw data preparation and processing steps were consistent between the software packages, and most of the deviations in the estimated fluxes were due to the flux corrections. Among the different calculation procedures analysed, the spectral correction had biggest impact for closed-path latent heat fluxes, reaching nocturnal median value of 15% at the wetland site. We found up to 43% median value of deviation (with respect to the run with all corrections included) if closed path carbon dioxide flux is calculated without the dilution correction, while the methane fluxes were up to 10% lower without both dilution and spectroscopic corrections. The density (and spectroscopic) correction was the most critical step for open-path systems. However, we found also large spectral correction factors for the open-path methane fluxes, due to the sensor separation effect.