Carob is a legume tree of a considerable commercial importance for the flavor and sweet industry. In this context, it is cultivated mostly for its pods, which are known for their nutritive value and multiple health benefits. However, metabolite patterns, underlying these properties are still mostly uncharacterized. In this study, the role of geographical origin, ontogenetic changes and thermal processing on the Ceratonia siliqua pod metabolome was assessed by mass spectrometry (MS)-based metabolomics. Thereby, a total of 70 fruits primary metabolites, represented mainly by carbohydrates, organic and amino acids were detected. Analysis of secondary bioactive metabolites assessed by ultra-high-performance liquid chromatography-electrospray ionization high resolution mass spectrometry (UHPLC-ESI-HR-MS) revealed in total 83 signals. The major signals, most significantly contributing in discrimination of C. siliqua specimens were assigned to tannins and flavonoids. PCA models derived from either UHPLC-MS or GC-MS proved to be powerful tools for discrimination of C. siliqua specimens.