Significance Nucleation is ubiquitous in many natural and industrial processes, yet our understanding of how a nucleus first emerges is limited. According to classical nucleation theory, a nucleus from which crystals grow forms in a single, spontaneous step. In this work, we combine ultralow-dose in situ liquid-phase and cryogenic transmission electron microscopy to show that metal–organic frameworks (MOFs) nucleate through a different, nonclassical pathway with three distinct steps. These steps are phase separation, condensation, and crystallization. Our observations of intermediate steps during the crystallization of MOFs provide important insight for controlling the nucleation and growth of both crystalline and amorphous materials.