Silicon nitride (Si3N4) ceramics are used in numerous applications because of their superior mechanical properties. Their intrinsically brittle nature is a critical issue, but can be overcome by introducing whisker-like microstructural features. However, the formation of such anisotropic grains is very sensitive to the type of cations used as the sintering additives. Understanding the origin of dopant effects, central to the design of high-performance Si3N4 ceramics, has been sought for many years. Here we show direct images of dopant atoms (La) within the nanometre-scale intergranular amorphous films typically found at grain boundaries, using aberration corrected Z-contrast scanning transmission electron microscopy. It is clearly shown that the La atoms preferentially segregate to the amorphous/crystal interfaces. First-principles calculations confirm the strong preference of La for the crystalline surfaces, which is essential for forming elongated grains and a toughened microstructure. Whereas principles of micrometre-scale structural design are currently used to improve the mechanical properties of ceramics, this work represents a step towards the atomic-level structural engineering required for the next generation of ceramics.