Farnesol (FAR) belongs to terpenes group and is a sesquiterpene alcohol and a hydrophobic compound, which can be extracted from natural sources or obtained by organic chemical or biological synthesis. Recent advances in the field of nanotechnology allow the drawbacks of low drug solubility, which can improve the drug therapeutic index. Therefore, this study aimed to prepare the FAR inclusion complexes with β-cyclodextrin (β-CD) and hydroxypropyl-β-cyclodextrin (HP-β-CD) through freeze-drying method, proposing their physicochemical characterization, comparing their toxicity, and evaluating their in vitro antibacterial activity. Initially, physical mixture and freeze-dried inclusion complexes of FAR/β-CD and FAR/HP-β-CD were obtained in the molar ratio (1:1). The samples were characterized by DSC, TG/DTG, FTIR, PXRD, SEM, pH