We present a variational formulation for the Navier-Stokes-Fourier system based on a free energy Lagrangian. This formulation is a systematic infinite dimensional extension of the variational approach to the thermodynamics of discrete systems using the free energy, which complements the Lagrangian variational formulation using the internal energy developed in cite{GBYo2016b} as one employs temperature, rather than entropy, as an independent variable. The variational derivation is first expressed in the material (or Lagrangian) representation, from which the spatial (or Eulerian) representation is deduced. The variational framework is intrinsically written in a differential-geometric form that allows the treatment of the Navier-Stokes-Fourier system on Riemannian manifolds.