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Temperature fluctuation commonly occurs in the cold chain leading to complete or partial thawing and refreezing of frozen products resulting in a multifrozen product. Such oscillation of temperature could cause significant quality reduction compared to single frozen products. This study was designed to differentiate frozen Atlantic salmon fillets based on the level of temperature fluctuation. Near‐infrared spectroscopy (NIRS) coupled with chemometrics was used to classify the frozen fillets stored at no fluctuation (NF), low fluctuation (LF), high fluctuation (HF), and very high fluctuation (VF) temperature. Using spectral profiles obtained at both frozen and thawed states, fillets were classified based on the level of temperature fluctuation by partial least squares discriminant analysis (PLS‐DA). The thawed samples showed better classification accuracy (71%) than frozen samples (66%) in a four‐class model. Considering the small variation within the first two (NF, LF) and the last two (HF, VF) groups, a two‐class classification model was developed using thawed samples, and the obtained model correctly classified the two groups ([NF, LF] and [HF, VF]) with 100 % classification accuracy. Protein‐ and water‐related changes were found important to distinguish the fillets. Based on these findings, the four‐class prediction model is found insufficient to be used for nondestructive determination of temperature history of frozen fillets. However, the two‐class prediction model with further external validation can be applied to determine the level of temperature fluctuation particularly using fillets scanned at thawed state. Practical Application: NIR spectroscopy can be used to evaluate the degree of temperature fluctuation and thus related quality loss throughout the logistics of frozen Atlantic salmon fillets. Researchers, food control authorities, and the retail industry could be the primary beneficiaries of this research output. [ABSTRACT FROM AUTHOR]