TDP-43 is a model protein for pathophysiological phase transitions, forming a multitude of intracellular assemblies with different physical properties. Physiological condensation is widely presumed to precede pathological aggregation, but the causal relationships between different modes of assembly in vivo are still unclear. Here we use Distributed Amphifluoric FRET (DAmFRET) and complementary approaches to map the phase space of TDP-43 self-assembly in yeast cells. We discovered that the low-complexity C-terminal domain (CTD) on its own populates dynamically arrested soluble clusters rather than condensates. These clusters uniquely supported amyloid formation, and only when templated by pre-existing amyloids of other proteins. Other features of full-length TDP-43, pathological C-terminal fragments, or fusion partners that self-interacted blocked amyloid nucleation by allowing CTD clusters to further condense. Stress and cotranslational condensation had the same effect. Our findings reveal that TDP-43 amyloid formation occurs only under very specific physical and biological circumstances that could present new opportunities for therapeutic control.