We study the long-time decay of rotating turbulence in Bose-Einstein condensates (BECs). We consider the Gross-Pitaevskii equation in a rotating frame of reference, and review different formulations for the Hamiltonian of a rotating BEC. We discuss how the energy can be decomposed, and present a method to generate out-of-equilibrium initial conditions. We also present a method to generate finite-temperature states of rotating BECs compatible with the Canonical or the Grand canonical ensembles. Finally, we integrate numerically rotating BECs in cigar-shaped traps. A transition is found in the system dynamics as the rotation rate is increased, with a final state of the decay of the turbulent flow compatible with an Abrikosov lattice in a finite-temperature thermalized state.