Dataset containing final processed and gap-filled eddy covariance and meteorological data corresponding to the publication "Does increased spatial replication above heterogeneous agroforestry improve the representativeness of eddy covariance measurements?", to be submitted soon to Biogeosciences from Copernicus. There is one file corresponding to each station. Quality flags were developped for gap-filled data, both for eddy covariance and meteorological measurements, as described in the article. The supporting file "variable_names_units" contains information on the units of each variable and describes the variable. Precipitation data are submitted separately because the time resolution is 1h, due to how the gap-filling was performed (please look at publication for more details on it). All variables necessary for footprint analysis are in the files. The folder footprint_by_seasons.zip contains the coordinates of the 80 % footprint contour lines, for all five seasons and all four stations, necessary for figure 3. Additionally, the Python code used to analyze the results and plot the figures for the paper (except for the maps of land cover and footprints) is published. In few months, the whole code used to gap fill both meteorological and flux data, as well as to partition carbon dioxide flux, will be available at a different repository, linked to a data publication.