Nickel implanted silicon substrate shows potential applications for the fabrication of infrared detectors, solar cells, spintronic devices as well as for the synthesis of an embedded nickel silicide layer inside Si substrates. Emerging applications of the transition metal implanted silicon structures for the fabrication of intermediate band materials motivated us to study the in-depth distribution profile of Ni ions as well as the structural changes that occur at the top of silicon substrate surface before and after annealing process. In the present work, we have carried out detailed study on the crystalline silicon substrates, implanted with Ni− ions comprising ion dose value of 5 × 1016 ions/cm2 at 100 keV implantation energy followed with the post implantation annealing at 800 °C temperature for a time duration of 2 h. The distribution profile of nickel ions inside the silicon substrate was estimated using the non-destructive simultaneous XRR-GIXRF measurements and were also compared with results obtained from the RBS and SIMS measurements. The in-depth concentration profile of Ni ions inside Si substrate derived from XRR-GIXRF measurements was found to be in close agreement with that of obtained from the RBS measurements. Furthermore, our investigations clearly showed that the annealing process causes the inward and outward diffusion of the Ni atoms inside the Si substrate, thus significantly changing the in-depth concentration profile of Ni ions in the Si matrix. The XANES and EXAFS results also demonstrate the formation of NiSi2 phase around Ni atoms in the implanted region of Si 〈100〉 substrate.