AbstractTailoring nanoparticles’ composition and morphology is of particular interest for improving their performance for catalysis. A challenge of this approach is that the nanoparticles’ optimized initial structure often changes during use. Visualizing the three dimensional (3D) structural transformation in situ is therefore critical, but often prohibitively difficult experimentally. Although electron tomography provides opportunities for 3D imaging, restrictions in the tilt range of in situ holders together with electron dose considerations limit the possibilities for in situ electron tomography studies. Here, an in situ 3D imaging methodology is presented using single particle reconstruction (SPR) that allows 3D reconstruction of nanoparticles with controlled electron dose and without tilting the microscope stage. This in situ SPR methodology is employed to investigate the restructuring and elemental redistribution within a population of PtNi nanoparticles at elevated temperatures. The atomic structure of PtNi is further examined and a heat‐induced transition is found from a disordered to an ordered phase. Changes in structure and elemental distribution are linked to a loss of catalytic activity in the oxygen reduction reaction. The in situ SPR methodology employed here can be extended to a wide range of in situ studies employing not only heating, but gaseous, aqueous, or electrochemical environments to reveal in‐operando nanoparticle evolution in 3D.