Natural ecosystems are composed of heterogeneous landscapes challenging CO₂ fluxes quantification per landcover type. Here, we combine UAV (Uncrewed Aerial Vehicle) measurements of CO₂ gas concentrations with a Large-Eddy simulation model in a sub-mesoscale inversion to separate fluxes by landcover type, demonstrating a promising approach to capture and upscale flux heterogeneity within eddy-covariance footprints.