The co-implantation of F and B in pre-amorphized Si has been proved to be beneficial for the fabrication of ultrashallow junctions due to a remarkable reduction of B diffusion. This is attributed to the presence of fluorine-vacancy (F–V) complexes after regrowth, acting as annihilation centers for Si interstitials. Whereas the resulting F profile in the recrystallized layer can be easily determined by chemical profiling, the vacancy distribution, which has a strong influence on B diffusion, can only be indirectly estimated. In this work, atomistic simulations have been used to analyze several aspects that can affect the efficiency of F–V complexes on Si interstitials annihilation, by considering the effects on B diffusion and the evolution of F profiles. The vacancy content of the complexes, determined by the F/V ratio, and the complex size play an important role on B redistribution. The existence of a recombination barrier for the interaction of a Si interstitial and some F–V complexes, as proposed by theoretical calculations, and its influence on the Si interstitial annihilation efficiency of the complexes are also analyzed.