Cu6Sn5 is one of the most important intermetallics present in solder joints based on Cu and Sn. Due to still uncertain reasons for failure of these joints, detailed microstructural research can help to figure out the underlying mechanisms. For Cu- and as well for Sn-rich environments of the Cu6Sn5 the microstructural occurrence of the phase transformations are investigated. During the formation of stable η′ from the disordered high temperature η phase the formation of metastable modulated incommensurately ordered η′′ takes place. For the copper rich samples long-range ordering and twin-related domain formation within η′′ was observed. Although conventional Hough-based EBSD analysis was not able to identify the correct domain orientation, Kikuchi pattern matching using simulated patterns was able to resolve the correct microstructure. As ordered intermetallics tend to be brittle in nature, the current microstructure research provides a basis to investigate unresolved problems in the initiation of failure.