Context: The anomalously large radii of hot Jupiters has long been a mystery. However, by combining both theoretical arguments and 2D models, a recent study has suggested that the vertical advection of potential temperature leads to an adiabatic temperature profile in the deep atmosphere hotter than the profile obtained with standard 1D models. Aims: In order to confirm the viability of that scenario, we extend this investigation to three dimensional, time-dependent, models. Methods: We use a 3D GCM, DYNAMICO to perform a series of calculations designed to explore the formation and structure of the driving atmospheric circulations, and detail how it responds to changes in both upper and deep atmospheric forcing. Results: In agreement with the previous, 2D, study, we find that a hot adiabat is the natural outcome of the long-term evolution of the deep atmosphere. Integration times of order $1500$ years are needed for that adiabat to emerge from an isothermal atmosphere, explaining why it has not been found in previous hot Jupiter studies. Models initialised from a hotter deep atmosphere tend to evolve faster toward the same final state. We also find that the deep adiabat is stable against low-levels of deep heating and cooling, as long as the Newtonian cooling time-scale is longer than $sim 3000$ years at $200$ bar. Conclusions: We conclude that the steady-state vertical advection of potential temperature by deep atmospheric circulations constitutes a robust mechanism to explain hot Jupiter inflated radii. We suggest that future studies of hot Jupiters are evolved for a longer time than currently done, and, when possible, include models initialised with a hot deep adiabat. We stress that this mechanism stems from the advection of entropy by irradiation induced mass flows and does not require (finely tuned) dissipative process, in contrast with most previously suggested scenarios.