The linear and non-linear thermoelectric properties of molecular junctions are theoretically studied close to room temperature within a model including electron-electron and electron-vibration interactions on the molecule. A non-equilibrium adiabatic approach is devised to include a strong Coulomb repulsion and applied to the self-consistent calculation of electron and phonon transport properties of massive molecules, such as fullerenes, within the Coulomb blockade regime. We show that the phonon thermal conductance is quite sensitive to strong electron-electron interactions within the intermediate electron-vibration coupling regime. Furthermore, the electron-vibration interaction enhances both phonon and electron thermal conductance, and it reduces not only the charge conductance, but also the thermopower. The effect of the strong electron-electron interactions provides a peculiar double-peak structure to the thermopower versus charge conductance curve. Finally, within the regime of weak to intermediate electron-vibration and vibration-lead phonon coupling, the peak values of the thermoelectric figure of merit are slightly less than unity, and the maximal efficiency of the junction can reach values slightly less than half of the Carnot limit for large temperature differences between the leads. Recently, the possibility of controlling materials at the nanoscale has been exploited to optimize the thermoelectric efficiency [4,6,7]. For example, a maximum ZT 2.4 ≃ has been observed at room temperature in Bi Te Sb Te 2 3 2 3 superlattice thermoelectric devices [8]. High values of ZT have been reported in quantum dot superlattices [9] and in semiconductor nanowires [10], where phonon confinement can lead to a lower phonon thermal conductance [11,12]. Actually, a significant reduction in lattice thermal conductivity is considered as the main route for having high ZT in low-dimensional materials [13]. The improvement of thermoelectric efficiency can also derive from the discreteness of energy levels in nanostructures resulting into a violation of the OPEN ACCESS