The effect of secondary sintering additives and/or a post-sintering heat treatment on the semicrystalline atomic structure of the intergranular phase in silicon nitride ceramics is investigated. Three different Yb-doped Si3N4 ceramic compositions are examined using a scanning transmission electron microscope, whereby the intergranular atomic structure is directly imaged with Ångstrom resolution. The resulting high-resolution images show that the atomic arrangement of the Yb takes very periodic positions along the interface between the intergranular phase and the matrix grains, and that a postsintering 1250°C heat treatment, as well as a change of the secondary sintering additives (Al2O3 vs SiO2), does not alter the atomic positions of Yb. This result has implications for the understanding of how the mechanical properties of ceramics are influenced by the presence of the nanoscale intergranular phase, and for associated computational modeling of its precise role and atomic structure.