Abstract. Carbonyl sulfide (COS) flux measurements with the eddy covariance (EC) technique are becoming popular for estimating gross primary productivity. To compare COS flux measurements across sites, we need standardized protocols for data processing. In this study, we analyze how various data processing steps affect the calculated COS flux and how they differ from carbon dioxide (CO2) flux processing steps, and we provide a method for gap-filling COS fluxes. Different methods for determining the time lag between COS mixing ratio and the vertical wind velocity (w) resulted in a maximum of 15.9 % difference in the median COS flux over the whole measurement period. Due to limited COS measurement precision, small COS fluxes (below approximately 3 pmol m−2 s−1) could not be detected when the time lag was determined from maximizing the covariance between COS and w. The difference between two high-frequency spectral corrections was 2.7 % in COS flux calculations, whereas omitting the high-frequency spectral correction resulted in a 14.2 % lower median flux, and different detrending methods caused a spread of 6.2 %. Relative total uncertainty was more than 5 times higher for low COS fluxes (lower than ±3 pmol m−2 s−1) than for low CO2 fluxes (lower than ±1.5 µmol m−2 s−1), indicating a low signal-to-noise ratio of COS fluxes. Due to similarities in ecosystem COS and CO2 exchange, we recommend applying storage change flux correction and friction velocity filtering as usual in EC flux processing, but due to the low signal-to-noise ratio of COS fluxes, we recommend using CO2 data for time lag and high-frequency corrections of COS fluxes due to the higher signal-to-noise ratio of CO2 measurements.