The thin intergranular phase in a silicon nitride (Si3N4) ceramic, which has been regarded for decades as having an entirely amorphous morphology, is shown to have a semi-crystalline structure. Using two different but complementary high-resolution electron microscopy methods, the intergranular atomic structure was directly imaged at the atomic level. These high-resolution images show that the atomic arrangement of the dopand element cerium takes very periodic positions not only along the interface between the intergranular phase and the Si3N4 matrix grains, but it arranges in a semi-crystalline structure that spans the entire width of the intergranular phase between two adjacent matrix grains, in principle connecting the two separate matrix grains. The result will have implications on the approach of understanding the materials properties of ceramics, most significantly on the mechanical properties and the associated computational modelling of the atomic structure of the thin intergranular phase in Si3N4 ceramics.