Understanding and controlling microscopic heat transfer mechanisms in solids is critical to material design in numerous technological applications. Yet, the current understanding of thermal transport in semiconductors and insulators is limited by the difficulty in directly measuring individual phonon lifetimes and mean free paths, and studying their dependence on the microscopic state of the material. Here we report our measurements of microscopic phonon scattering rates in AgBiSe2, which exhibits a controllable, reversible change directly linked to microstructure evolution near a reversible structural phase transition, that directly impacts the thermal conductivity. We demonstrate a steplike doubling of phonon scattering rates resultant from the cation disordering at the structural transition. To rationalize the neutron scattering data, we leverage a stepwise approach to account for alterations to the thermal conductivity that are imparted by distinct scattering mechanisms. These results highlight the potential of tunable microstructures housed in a stable crystal matrix to provide a practical route to tailor phonon scattering to optimize thermal transport properties.