Controlling the grain boundary network of small-scale materials—such as coatings and thin films—is an ambitious goal that would ultimately enable the production of components with tailored properties and improved reliability. In this work we present a new technique—which we term ion-induced grain boundary engineering (iGBE)—to engineer the character distribution and connectivity of grain boundaries in gold films in situ, as they are being deposited. iGBE consists of a repeated sequence of ion-induced material removal and material deposition which results in the selection and growth of crystal grains in twinned relationship. This phenomenon yields a substantial increase in the density and connectivity of Σ3 twin boundaries, which have renowned beneficial effects on the material's resistance to intergranular degradation. We confirm the improved reliability of iGBE microstructures by assessing their resistance to electromigration—one of the most common causes of failure in integrated circuit interconnects. We find that, through iGBE, interconnect lifetime increases by three orders of magnitude at standard operating conditions. Since iGBE is material-insensitive and compatible with standard microfabrication technology, we expect it to have significant impact on microelectronics industry.