Mediterranean plant Helichrysum italicum represents a rich source of versatile bioactive compounds with potential benefits for human health. Despite extensive research on the plant’s active constituents, little attention has yet been paid to characterizing the relationship between its intra-specific genetic diversity and metabolite profile. The study aimed to determine metabolic profile of H. italicum ssp. italicum (HII) and ssp. tyrrhenicum (HIT) cultivated on the experimental plantation in Slovenia and to compare the chemical composition of extracts regarding the solvent extraction process. Extracts were prepared upon conventional extract preparation procedures: maceration with 50% methanol or ethanol and cold or hot water infusion and analyzed using High Performance Liquid Chromatography-Diode Array Detection-Electrospray Ionization-Quadrupole Time-of-Flight-Mass Spectrometry (HPLC-DAD-ESI-QTOF-MS). One hundred compounds were identified in the samples, among them several isomers and derivatives were reported for the first time, while caffeoylquinic acids and pyrones were the most abundant. Semi-quantitative comparison revealed that the extraction procedure had a greater impact on the chemical profile than genetic variability. All HIT extracts showed a higher total phenolic content compared to HII, while the antioxidant potential evaluated by 1,1-diphenyl-2-picrylhydrazil test was not proportionally higher. In addition, hot water extracts proved to be comparably active as alcoholic ones, confirming high commercial potential of Helichrysum italicum as herbal functional beverages.