We assess heat and mass transfer limitations in in situ studies of model catalysts with a first-principles based multiscale modeling approach that integrates a detailed description of the surface reaction chemistry and the macro-scale flow structures. Using the CO oxidation at RuO2(110) as a prototypical example we demonstrate that factors like a suppressed heat conduction at the backside of the thin single-crystal, and the build-up of a product boundary layer above the flat-faced surface play a significant role.