The exchange of momentum, heat and trace gases between atmosphere and surface is mainly controlled by turbulent fluxes. Turbulent mixing is usually parametrized using Monin–Obukhov similarity theory (MOST), which was derived for steady turbulence over homogeneous and flat surfaces, but is nevertheless routinely applied to unsteady turbulence over non-homogeneous surfaces. We study four years of eddy-covariance measurements at a highly heterogeneous alpine valley site in Finse, Norway, to gain insights into the validity of MOST, the turbulent transport mechanisms and the contributing coherent structures. The site exhibits a bimodal topography-following flux footprint, with the two dominant wind sectors characterized by organized and strongly negative momentum flux, but different anisotropy and contributions of submeso-scale motions, leading to a failure of eddy-diffusivity closures and different transfer efficiencies for different scalars. The quadrant analysis of the momentum flux reveals that under stable conditions sweeps transport more momentum than the more frequently occurring ejections, while the opposite is observed under unstable stratification. From quadrant analysis, we derive the ratio of the amount of disorganized to organized structures, that we refer to as organization ratio (OR). We find an invertible relation between transfer efficiency and corresponding organization ratio with an algebraic sigmoid function. The organization ratio further explains the scatter around scaling functions used in MOST and thus indicates that coherent structures modify MOST. Our results highlight the critical role of coherent structures in turbulent transport in heterogeneous tundra environments and may help to find new parametrizations for numerical weather prediction or climate models.