Eddy Covariance technique is rapidly spreading all over the world as a strong direct method to measure turbulent fluxes of energy and matter between ecosystems and atmosphere: nonetheless there is not yet a standardization of post-field data processing sequences. Since there are many different possible methodologies to treat raw data, it’s becoming more and more important to assess uncertainties arising from post-field data processing. Our goal is to analyse the effects of the most relevant processing steps applied to raw data, quantifying their relative contribution to the total uncertainties.