The atomic arrangement in certain ordered alloys, such as B2–Fe₆₀Al₄₀ determines intrinsic material properties for instance, the saturation magnetization. Here we have investigated the influence of open-volume defects on the atomic ordering process at elevated temperatures in Fe₆₀Al₄₀ thin films. A dependence of the ordering process on the type and concentration of defects is observed by positron annihilation spectroscopy combined with ab-initio calculations. Comparing the lifetimes of positrons in the alloy for different annealing and irradiation treatments reveals the role of mono-vacancies, triple defects as well as large vacancy clusters: The rate of atomic ordering to the ordered B2 state is increased in the presence of mono-vacancies whereas triple defects and vacancy complexes decrease the ordering rate. Furthermore, an agglomeration of vacancies during annealing to di-vacancies and larger vacancy clusters is observed. The distribution of open-volume defects can be modified in such a way as to control the thermal stability via ion-irradiation and thermal pre-treatments.