The structural and microstructural evolution of microwave plasma nitrided SrTiO3 was studied by scanning, high-resolution transmission electron microscopy (STEM, HRTEM), electron energy loss spectroscopy, and energy dispersion X-ray spectroscopy (EELS/EDX) combined with elemental mapping at the nanometer scale. EELS/EDX mappings show the SrTiO3-xNy single crystal formation as well as the TiN1-xOy. nanograin layer formation on the surface, which depends on the plasma treatments. Stacking faults were the most common defects found in single crystal SrTiO3-xNy either with SrO plane-excess or TiO2 plane-excess. The excess of SrO was integrated as Ruddlesden-Popper planar faults, showing an arrangement of the three-dimensional nanostructure, and the excess of TiO2-xNy was integrated as crystallographic shear defects. Nitrogen incorporation into the structure is not homogeneous at the atomic level, and a high concentration of nitrogen was found in Sr-deficient planar defects.