Nanocrystalline metals display interesting basic and technological properties related to their chemical and structural properties. Among other properties, they display a richer phase diagram due to the additional degree of freedom introduced by the nanoparticles surface. Metal nanoparticles encapsulated within biological macromolecules have the additional advantage of biocompatibility. In this paper we investigate the thermal evolution of the structure and dynamics of apoferritin encapsulated nanocrystalline copper. We determined the occurrence of a yet unexpected phase transition from a low temperature FCC to a complex high temperature phase including a (putative) amorphous precursor. The occurrence of a FCC-icosahedral transition is also discussed as a possible explanation to our results. The lattice dynamics of the FCC phase (monitored by its Debye temperature) differs from the behaviour expected for nanosized structures.