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Benzo[a]pyrene (BaP), a key polycyclic aromatic hydrocarbon (PAH) often associated with soot particles coated by organic compounds, is a known carcinogen and mutagen. When mixed with organics, the kinetics and mechanisms of chemical transformations of BaP by ozone in indoor and outdoor environments are still not fully elucidated. Using direct analysis in real-time mass spectrometry (DART-MS), kinetics studies of the ozonolysis of BaP in thin films exhibited fast initial loss of BaP followed by a slower decay at long exposure times. Kinetic multilayer modeling demonstrates that the slow decay of BaP over long times can be simulated if there is slow diffusion of BaP from the film interior to the surface, resolving long-standing unresolved observations of incomplete PAH decay upon prolonged ozone exposure. Phase separation drives the slow diffusion time scales in multicomponent systems. Specifically, thermodynamic modeling predicts that BaP phase separates from secondary organic aerosol material so that the BaP-rich layer at the surface shields the inner BaP from ozone. Also, BaP is miscible with organic oils such as squalane, linoleic acid, and cooking oil, but its oxidation products are virtually immiscible, resulting in the formation of a viscous surface crust that hinders diffusion of BaP from the film interior to the surface. These findings imply that phase separation and slow diffusion significantly prolong the chemical lifetime of PAHs, affecting long-range transport of PAHs in the atmosphere and their fates in indoor environments.