This study aimed at quantifying potential negative effects of instrument heating to improve eddy-covariance flux data quality in cold environments. Our overarching objective was to minimize heating-related bias in annual CO₂ budgets from an Arctic permafrost system. We used continuous eddy-covariance measurements covering three full years within an Arctic permafrost ecosystem with parallel sonic anemometers operation with activated heating and without heating as well as parallel operation of open- and closed-path gas analyzers, the latter serving as a reference. Our results demonstrate that the sonic anemometer heating has a direct effect on temperature measurements while the turbulent wind field is not affected. As a consequence, fluxes of sensible heat are increased by an average 5 W m^-2 with activated heating, while no direct effect on other scalar fluxes was observed. However, the biased measurements in sensible heat fluxes can have an indirect effect on the CO₂ fluxes in case they are used as input for a density-flux WPL correction of an open-path gas analyzer. Evaluating the self-heating effect of the open-path gas analyzer by comparing CO₂ flux measurements between open- and closed-path gas analyzers, we found systematically higher CO2 uptake recorded with the open-path sensor, leading to a cumulative annual offset of 96 gC m^-2, which was not only the result of the cold winter season but also due to substantial self-heating effects during summer. With an inclined sensor mounting, only a fraction of the self-heating correction for vertically mounted instruments is required.