In situ techniques of transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS) were used to investigate the thermal stability of Ni−Co core−shell nanoparticles (NPs). The morphological, structural, and chemical changes involved in the core− shell reconfiguration were studied during in situ annealing through simultaneous imaging and acquisition of elemental maps in the TEM, and acquisition of O 1s, Ni 3p, and Co 3p XP spectra. The core−shell reconfiguration occurred in a stepwise process of surface oxide removal and metal segregation. Reduction of the stabilizing surface oxide occurred from 320 to 440°C, initiating the core−shell reconfiguration. Above 440°C, the core−shell structure was disrupted through Ni migration from the core to the shell. This resulted in the formation of a homogeneous Ni−Co mixed alloy at 600°C. This study provides a mechanistic description of the alteration in the core−shell structures of NPs under vacuum conditions and increasing annealing temperature, which is crucial for understanding these technologically important materials.