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Saponaria sicula Raf. grows in Sicily, Sardinia, and Algeria on limestone cliffs and volcanic sands 1300–2500 m above sea level. The aim of the present study was to investigate how the pedo-climatic conditions influence the micromorphological, phytochemical, and biological properties of Sicilian S. sicula leaves collected in the Madonie Mountains (SsM) and on Etna Mt (SsE). Micromorphological investigations revealed that leaves from SsM had a higher amount of calcium oxalate druses in the mesophyll and a more intense blue–green staining with Toluidine blue O, indicating a higher content of polyphenols. These data were confirmed by phytochemical analyses carried out on hydroalcoholic extracts, which showed a higher content of total phenols (8.56 ± 0.57 g GAE/100 g DE) and flavonoids (6.09 ± 0.17 g RE/100 g DE) in SsM. Sixty-four compounds were identified by LC-DAD-ESI-MS analysis with propelargonidin dimer as the most abundant compound (10.49% and 10.19% in SsM and SsE, respectively). The higher polyphenol content of SsM leaves matches also with their biological activity, identifying SsM extract as the strongest plant complex (IC50 2.75–477.30 µg/mL). In conclusion, the present study experimentally demonstrates that not only climatic differences but also soil characteristics affect the micromorphological, phytochemical, and biological features of this plant species. [ABSTRACT FROM AUTHOR]