Interfaces in as-processed β-Yb2Si2O7 environmental barrier coating (EBC) ceramics, and those after high-temperature (1500 °C) interaction with a calcia-magnesia-aluminosilicate (CMAS) glass from Part I are studied in further detail using high-resolution transmission electron microscopy (HRTEM), annular dark field scanning TEM (ADF STEM) and high-angle ADF (HAADF) STEM. Disconnections are detected, or inferred, at twin and general grain-boundaries and also at phase boundaries. Grain-boundary and facet planes are found to be aligned parallel to {110} planes of β-Yb2Si2O7. When detected, step planes are also found to be aligned parallel to β-Yb2Si2O7 {110} planes. At the same time, the dislocation component has major projections aligned parallel to {110} planes of β-Yb2Si2O7. As such, both the step and the dislocation components of the disconnections are anisotropic. The tendency of the grain-boundary and facet planes at interfaces in the system to align parallel to β-Yb2Si2O7{110} planes, both before and after CMAS-interaction, is discussed. The chemistry of grain-boundaries in the vicinity of the disconnections is found to be non-stoichiometric, but this by itself cannot account for the extended contrast variations along twin boundaries. Thus, contrast variations along grain boundaries are associated mainly with the presence of disconnections and associated strain, as well as long-range distortions in the unit cells in twin boundaries. These anisotropic disconnections are associated with the mechanisms of grain-boundary and phase-boundary migration, and thus, they have implications on the evolution of microstructures in this system. Combined insights from Part I and this Part II elucidate the nature of the interfaces in β-Yb2Si2O7 EBC ceramic and the mechanisms of CMAS glass penetration.