Turbulent superstructures, i.e. large-scale flow structures in turbulent flows, play a crucial role in many geo- and astrophysical settings. In turbulent Rayleigh–Bénard convection, for example, horizontally extended coherent large-scale convection rolls emerge. Currently, a detailed understanding of the interplay of small-scale turbulent fluctuations and large-scale coherent structures is missing. Here, we investigate the resolved kinetic energy and temperature variance budgets by applying a filtering approach to direct numerical simulations of Rayleigh–Bénard convection at high aspect ratio. In particular, we focus on the energy transfer rate between large-scale flow structures and small-scale fluctuations. We show that the small scales primarily act as a dissipation for the superstructures. However, we find that the height-dependent energy transfer rate has a complex structure with distinct bulk and boundary layer features. Additionally, we observe that the heat transfer between scales mainly occurs close to the thermal boundary layer. Our results clarify the interplay of superstructures and turbulent fluctuations and may help to guide the development of an effective description of large-scale flow features in terms of reduced-order models.