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Recent studies have dealt about the phenolic compounds and the nutraceutical properties of Sanguisorba minor Scop and about the possibility of their domestication to standardise the plant production. However, it is also known that the storage conditions can affect the bioactive compounds present in plants. Thus, wild (W) and domesticated (F1, F2, F3) S. minor samples were exposed to different drying methods (oven-drying at 60 °C until constant weight named OD or freeze-drying until constant weight named FD) and studied for their content in phenolic compounds, antioxidant, antimicrobial, cytotoxic and anti-inflammatory properties. In general, OD samples showed the highest nutraceutical properties and the highest content in phenolic compounds. The most abundant phenolic compounds in both drying methods were kaempferol-3-O-glucoside and caffeoyl ester, with some differences between wild and domesticated samples. Wild samples showed higher antimicrobial and cytotoxic activity than domesticated ones, except for the OD F3 and FD F2 samples that reported cytotoxicity against HeLa cells. This study provides important information to choose the most adequate methodology to retain phenolic compounds and nutraceutical properties of S. minor species. Further researches are necessary to standardise the domestication of the studied wild species and verify the highest efficiency of the OD method.