Nature Materials, Published online: 16 January 2026; doi:10.1038/s41563-025-02471-9Controllable and scalable phase transition of transition metal chalcogenides is challenging. Using in situ microscopic analysis, a non-stoichiometric phase transition from PdTe2 to PdTe is observed on the atomic scale, providing mechanistic insights into the scalable phase engineering of transition metal chalcogenide films and heterostructures.