Atomic-scale characterization of the intermetallic compound (IMC) layer often formed at the interfaces upon soldering has been performed. That IMC layer critically influences the subsequent functional performance and sustainability of the solder joints. Advanced atom probe tomography (APT) analysis was implemented on the IMC layer for the first time. Applying focused ion beam (FIB) sample preparation, thin lamellae were prepared from the desired region of the IMC layer at the interface of the copper substrate with the Sn-Ag solder alloy joint. In this work, iron nanoparticles were also used as reactive agents at the interface between the IMC layer and the copper substrate for controlling the growth kinetics of the IMC layer during the soldering reflow solidification. To this end, the results of the nano-scale characterization, specifically the APT elemental maps for different elements of Cu, Sn, Ag, and Fe from inside the IMC layer and in front of the IMC layer were analyzed to identify the nano-metric features of precipitates and elemental segregation at boundaries and their coherency with the IMC metal matrix. Accordingly, an atomic-scale model is proposed for the solidification progression of the IMC edge and concurrent reactive nano-scale precipitation through the IMC layer.