This work aimed the assessment of biochemical changes induced by laser or LED irradiation during mineralization of a bone defect in an animal model using a spectral model based on Raman spectroscopy. Six groups were studied: clot, laser (λ = 780 nm; 70 mW), LED (λ = 850 ± 10 nm; 150 mW), biomaterial (biphasic synthetic micro-granular hydroxyapatite (HA) + β-tricalcium phosphate), biomaterial + laser, and biomaterial + LED. When indicated, defects were further irradiated at a 48-h interval during 2 weeks (20 J/cm per session). At the 15th and 30th days, femurs were dissected and spectra of the defects were collected. Raman spectra were submitted to a model to estimate the relative amount of collagen, phosphate HA, and carbonate HA by using the spectra of pure collagen and biomaterials composed of phosphate and carbonate HA, respectively. The use of the biomaterial associated to phototherapy did not change the collagen formation at both 15 and 30 days. The amount of carbonate HA was not different in all groups at the 15th day. However, at the 30th day, there was a significant difference (ANOVA, p = 0.01), with lower carbonate HA for the group biomaterial + LED compared to biomaterial (p < 0.05). The phosphate HA was higher in the groups that received biomaterial grafts at the 15th day compared to clot (significant for the biomaterial; p < 0.01). At the 30th day, the phosphate HA was higher for the group biomaterial + laser, while this was lower for all the other groups. These results indicated that the use of laser phototherapy improved the repair of bone defects grafted with the biomaterial by increasing the deposition of phosphate HA.