Introduction The stress fractures (SFs) are a common condition in athletes and military recruits, characterized by partial fracture caused by repetitive applications of stresses that are lower than the stress required to fracture the bone in a single loading. Fourier transform infrared (FTIR) spectroscopy gives information about the bone composition and also can determine the amount of a molecule. For this reason, the FTIR spectroscopy may be used as a tool for diagnosis of certain bone diseases related to the bone strength. In this research, we established the contributions of mineral and collagen properties to SF risk through FTIR spectroscopy, analyzing the biochemical profile differences between the healthy bone and the bone with an SF. Materials and Methods Previous written informed consent was obtained, and samples of the hip with an SF (n = 11) and healthy bone from the femur with traumatic fracture (n = 5) were obtained and analyzed employing FTIR spectroscopy and its biochemical mapping function. Then, using FTIR spectra and the map, the collagen content and ratios corresponding to matrix maturity, mineralization, carbonate substitution, acid phosphate substitution, and crystallinity were calculated. Moreover, a histopathological analysis through Masson's staining was conducted. Results The biochemical analysis showed that the bone with an SF presented a bone immaturity characterized by a higher content of collagen, lower matrix maturity, mineralization, carbonate and acid phosphate substitutions, and greater crystallinity compared to the healthy bone, being checked by the ratio analysis and biochemical mapping. Besides, Masson's stain showed a higher collagen content in the bone with an SF. Conclusions The bone with an SF presented alterations in its biochemical composition, showing bone immaturity, which broadens the panorama of the condition to investigate future treatments or prophylactic techniques.