The advancement of techniques that can probe the behaviour of individual nanoscopic objects is of paramount importance in various disciplines, including photonics and electronics. As it provides images with a spatiotemporal resolution, four-dimensional electron microscopy, in principle, should enable the visualization of single-nanoparticle structural dynamics in real and reciprocal space. Here, we demonstrate the selectivity and sensitivity of the technique by visualizing the spin crossover dynamics of single, isolated metal–organic framework nanocrystals. By introducing a small aperture in the microscope, it was possible to follow the phase transition and the associated structural dynamics within a single particle. Its behaviour was observed to be distinct from that imaged by averaging over ensembles of heterogeneous nanoparticles. The approach reported here has potential applications in other nanosystems and those that undergo (bio)chemical transformations.