Germanium (Ge) is a promising semiconductor for on-chip photonics, but its monolithic integration on silicon (Si) platforms remains hindered by thermal processes incompatible with CMOS technology. Flash-lamp annealing (FLA) emerges as a viable solution to reduce defect densities in epitaxial Ge films while maintaining CMOS-compatible thermal budgets. We demonstrate that multi-pulse FLA (7.65 ms, 48.1 J/cm²) achieves dislocation density reduction in epitaxial Ge-on-Si equivalent to conventional high-temperature, long-duration annealing. We further show that FLA can serve as a tool for time-resolved investigation of defect dynamics during thermal processing, effectively freezing the material’s defect state at millisecond intervals. Our analysis reveals that excessive annealing temperatures trigger defect generation in Ge due to the relaxation of tensile strain arising from the Si–Ge thermal expansion mismatch during cooldown. Aberration-corrected scanning transmission electron microscopy indicates that this relaxation occurs through the splitting of misfit dislocations into partials bound by stacking faults, highlighting how strain relaxation pathways are directly influenced by annealing conditions. These results highlight the necessity of precise thermal management for optimizing defect structures in Ge and establish FLA as a scalable technique for defect engineering in group-IV semiconductors, paving the way for the integration of high-performance Ge photonic devices with Si technology.