In the microelectronic component industry, because of the miniaturization of functional units, the interaction of materials and interfaces play a much more significant role in their performance. The result of this is that ultrafine crystalline and trace impurity behavior impact a device’s operation to a much greater extent. This is the case with micro-connects for 3D integration, such as micro-bumps. Any unwanted crystalline behavior or interfacial segregated impurities can drastically alter a micro-connect’s performance, with a particular issue being intermetallic void formation, often known as Kirkendall voiding. Currently, it is unclear under what conditions voids form and how to prevent them. This work studies the microstructural and compositional differences between samples with different voiding densities. Results show that samples that exhibit an ultrafine crystalline have a higher propensity to exhibit voiding. Also, there is a high concentration of trace impurities located in the electrochemically deposited Cu layer. After isothermal annealing, high concentrations of impurities are located at the interface between Cu and the Cu–Sn intermetallic compound of Cu3Sn. An alternative explanation to the traditional Kirkendall void formation theory is presented. The explanation is based on the interaction of trace impurities from the electroplating process and the microstructural evolution.