Internal friction in oxide thin films imposes a critical limitation to the sensitivity and stability of ultra-high finesse optical cavities for gravitational wave detectors. Strategies like doping or creating nanolaminates are sought to introduce structural modifications that reduce internal friction. This work describes an investigation of the morphological changes SiO2/Ta2O5 and TiO2/Ta2O5 nanolaminates undergo with annealing and their impact on room temperature internal friction. It is demonstrated that thermal treatment results in a reduction of internal friction in both nanolaminates, but through different pathways. In the SiO2/Ta2O5 nanolaminate, which layers remain intact after annealing, the total reduction in internal friction follows the reduction in the composing SiO2 and Ta2O5 layers. Instead, interdiffusion initiated by annealing at the interface of the TiO2/Ta2O5 nanolaminate and the formation of a mixed phase dictate a more significant reduction in internal friction to ~ 2.6 * 10-4, a value lower than any other Ta2O5 mixture coating with similar cation concentration.