Inuloxin A is a promising plant phytotoxic sesquiterpene that deserves further studies to evaluate its potential as a bioherbicide. However, its low solubility in water and its bioavailability could hamper its practical applications. For this reason, inuloxin A was complexed with β-cyclodextrins by using three different methods, i.e., kneading, co-precipitation and grinding. The resulted complexes were fully characterized by different techniques such as 1H NMR, UV-vis, XRD, DSC and SEM, and they were biologically assayed in comparison with the pure compound in several biological systems. The efficacy of the kneading and grinding complexes was similar to that of inuloxin A and these complexes almost completely inhibit Phelipanche ramosa seed germination. The complete solubility in water and the preservation of the biological properties of these two complexes could allow further studies to develop a novel natural herbicide for parasitic plant management based on these formulations.