Recrystallization is essential for the synthesis of the highest quality Cu(In,Ga)Se2 (CIGSe) thin films for solar cell applications. Here we present a real-time study of the recrystallization of CIGSe thin films. We trigger the recrystallization by allowing diffusion of Cu into a Cu-poor CIGSe film and use synchrotron-based energy-dispersive X-ray diffraction to monitor this transition in real time. Additionally, we characterize the films by means of angle-dispersive X-ray diffraction. Before recrystallization, the X-ray diffraction patterns exhibit a signature that does not correspond to the ideal chalcopyrite structure of CIGSe. This signature can be attributed to stacking faults within the bulk of the films by modeling diffraction patterns of faulted CIGSe with the software DIFFaX. It is detected at temperatures below 650 K and is absent at temperatures above 750 K, which indicates that the faults in question were annihilated in this temperature range. This process occurs after the incorporation of Cu into the Cu-poor CIGSe lattice, which takes place in the 550–650 K temperature range.