The presynaptic active zone (AZ) is a precisely organized nanoscale domain where synaptic vesicle exocytosis and neurotransmitter release are governed by tightly regulated protein networks. This review synthesizes recent insights from electron microscopy (EM) and super-resolution fluorescence microscopy that have deepened our understanding of active zone architecture in mammalian central nervous system synapses and at the Drosophila neuromuscular junction (NMJ). These imaging techniques have elucidated the spatial organization of key active zone proteins relative to one another and to the plasma membrane, which is notably well-ordered at the Drosophila NMJ. Here, we present a detailed overview of the nanometer-scale positioning of AZ proteins across the two types of synapses. In parallel, the idea that active zone nanostructures may form through liquid–liquid phase separation has emerged as a potential organizing principle. The transient and dynamic interactions characteristic of phase-separated protein condensates contrast with models that attribute nanodomain organization to specific, stable protein–protein interactions, raising the question of how the active zone’s stable core architecture is reconciled with its capacity for dynamic plasticity.