The typical experimental conditions inside a transmission electron microscope (TEM), such as ultra-high vacuum, high-energy electron irradiation, and surface effects of ultrathin TEM specimens, can be the origin of unexpected microstructural changes compared with that of bulk material during in situ thermal-annealing experiments. In this paper, we report on the microstructural changes of a Fe–15%Si alloy during in situ TEM annealing, where, in its bulk form, it exhibits an ordering transformation from D03 to B2 at 650 °C. Using a heating-pot type double tilt holder with a proportional–integral–differential control system, we observed the precipitation of α-Fe both at the sample surface and inside the sample. Surface precipitates formed via surface diffusion are markedly large, several tens of nm, whereas precipitates inside the specimen, which are surrounded by Fe-poor regions, reach a maximum size of 20 nm. This unexpected microstructural evolution could be attributed to vacancies on Si sites, which are induced due to high-energy electron irradiation before heating, as well as enhanced thermal diffusion of Fe atoms.