Significance The true physical form of the proteins within the silk glands of spiders that permits storage at very high concentrations rather than as precipitated material prior to being transformed into solid silk fibers remains one of the fundamental mysteries that has limited our ability to produce artificial silks of the quality of natural silks. Here we determine that spider silk proteins are stored as complex micellar nanoparticles composed of assembled subdomains. When extruded during the silk spinning process, these subdomains undergo fibrillization while remaining assembled in micelles. Knowledge of the nanostructured protein assemblies in the dope is critical to the basic understanding of the spinning process and to our ability to mimic the natural material properties in synthetic analogues.