This study evaluates the feasibility of near infrared (NIR) spectroscopy to distinguish between different cartilage injury types associated with post-traumatic osteoarthritis and idiopathic osteoarthritis (OA) induced by mechanical and enzymatic damages. Bovine osteochondral samples (n = 72) were subjected to mechanical (n = 24) and enzymatic (n = 36) damage; NIR spectral measurements were acquired from each sample before and after damage, and from a separate control group (n = 12). Biomechanical measurements were then conducted to determine the functional integrity of the samples. NIR spectral variations resulting from different damage types were investigated and the samples classified using partial least squares discriminant analysis (PLS-DA). Partial least squares regression (PLSR) was then employed to investigate the relationship between the NIR spectra and biomechanical properties of the samples. Results of the study demonstrate that substantial spectral changes occur in the region of 1700–2200 nm due to tissue damages, while differences between enzymatically and mechanically induced damages can be observed mainly in the region of 1780–1810 nm. We conclude that NIR spectroscopy, combined with multivariate analysis, is capable of discriminating between cartilage injuries that mimic idiopathic OA and traumatic injuries based on specific spectral features. This information could be useful in determining the optimal treatment strategy during cartilage repair in arthroscopy.