The depth-dependent recovery of silicon thermal conductivity was achieved after the recrystallization of silicon that had been partially amorphized due to ion implantation. Transmission electron microscopy revealed nanoscale amorphous pockets throughout a structurally distorted band of crystalline material. The minimum thermal conductivity of as-implanted composite material was 2.46 W m−1 K−1 and was found to be uniform through the partially amorphized region. X-ray diffraction measurements reveal 60% strain recovery of the crystalline regions after annealing at 450 °C for 30 min and almost full strain recovery and complete recrystallization after annealing at 700 °C for 30 min. In addition to strain recovery, the amorphous band thickness reduced from 240 to 180 nm after the 450 °C step with nanoscale recrystallization within the amorphous band. A novel depth-dependent thermal conductivity measurement technique correlated thermal conductivity with the structural changes, where, upon annealing, the low thermal conductivity region decreases with the distorted layer thickness reduction and the transformed material shows bulk-like thermal conductivity. Full recovery of bulk-like thermal conductivity in silicon was achieved after annealing at 700 °C for 30 min. After the 700 °C anneal, extended defects remain at the implant projected range, but not elsewhere in the layer. Previous results showed that high point-defect density led to reduced thermal conductivity, but here, we show that point defects can either reform into the lattice or evolve into extended defects, such as dislocation loops, and these very localized, low-density defects do not have a significant deleterious impact on thermal conductivity in silicon.