Halloumi cheese has recently gained a Protected Designation of Origin (PDO) indicator, which is related to the place (Cyprus) in which halloumi cheese is made. The PDO label is linked with several requirements, e.g., milk species, quantities, etc.; thus, it is important to study this product regarding authenticity. The utility of using two spectroscopic techniques, hyperspectral imaging (HSI) (400–1000 nm) and conventional near-infrared spectroscopy (NIR) (800–2500 nm) were assessed for the discrimination of 17 Cypriot halloumi cheese types, which could be categorized as of cow or goat–sheep origin. The aim of this study was to obtain spectral information for halloumi cheese using other promising infrared and imaging spectroscopic techniques as a comparison to a previously acquired mid-infrared (MIR) spectroscopy dataset. NIR and HSI are both fast and easy techniques in application, both of which provide significant information in food analysis. Chemometric analysis was crucial for interpreting the spectroscopic data by applying the unsupervised methods: principal component analysis (PCA) and hierarchical cluster analysis (HCA). The HSI model was found to be based intuitively on the appearance of cheese samples after freeze-drying (e.g., color; yellow/white, and texture; oily/dry), while the NIR grouping of samples was determined to be based on composition, mainly fat, protein and lactose content of the cheese samples. The HSI model returned distinct clusters of the two halloumi cheese types, cow and goat–sheep origin, with one outlier (16/17 accuracy; 94%), while the NIR model proved less accurate (13/17; 76%).
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