A new field of application for high temperature nanoindentation as a complimentary method to understand the mechanics of plasticity upon bulk phase transformations in thermodynamic equilibrium is introduced. The feasibility is outlined on polycrystalline Cobalt involving a low-temperature hexagonal closed packed phase, and above 700K, a high-temperature face centered cubic phase, which was conventionally characterized by means of differential scanning calorimetry and high temperature X-ray diffraction. Strain rate sensitivity, activation volume and activation energy of plastic deformation were determined up to 873 K to identify the rate-controlling deformation mechanism. From RT to 473 K plasticity was found to be controlled by lattice friction on the basal plane, where dislocations have to overcome the Peierls barrier and deformation twinning was apparent in the hexagonal phase. The thermal activation of cross slip lead to reduced twinning actions when the phase transition temperature is approached. In the high temperature face centered cubic phase deformation was found to be controlled by cutting of forest dislocations and no deformation twinning was observed.