Thermally driven flows in fractures play a key role in enhancing the heat transfer and fluid mixing across the Earth’s lithosphere. Yet the energy pathways in such confined environments have not been characterised. Building on Letelier et al. (J. Fluid Mech., vol. 864, 2019, pp. 746–767), we introduce novel expressions for energy transfer rates – energetics – of geometrically constrained Rayleigh–Bénard convection in Hele-Shaw cells (HS-RBC) based on two different conceptual frameworks. First, we derived the energetics following the well-established framework introduced by Winters et al. (J. Fluid Mech., vol. 289, 1995, pp. 115–128), in which the gravitational potential energy, Ep, is decomposed into its available, Eap, and background, Ebp, components. Secondly, we derived the energetics considering a new decomposition for Ep, named dynamic, Edp, and reference, Erp, potential energies; Edp is defined as the departure of the system’s potential energy from the reference state Erp, determined by the ‘energy’ of the scalar fluctuations. For HS-RBC, both frameworks lead to the same energy transfer rates at a steady state, satisfying the relationship Eapτ = Edpτ + 1/6. Consistent with the work by Hughes et al. (J. Fluid Mech., vol. 729, 2013) on three-dimensional Rayleigh–Bénard convection, we report analytical expressions for the energetics and efficiencies of HS-RBC in terms of the Rayleigh number and the global Nusselt number. Additionally, we performed numerical experiments to illustrate the application of the energetics for the analysis of HS-RBC. Finally, we discuss the impact of the thermal forcing and the geometrical control exerted by Hele-Shaw cells on the development of boundary layers, protoplumes and the self-organisation of large-scale flows.