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Nitrapyrin (NP) is applied to cultivated soils to inhibit the enzymatic activity of ammonia monooxygenase (AMO), but its poor aqueous solubility and high volatility severely limit its application. β-Cyclodextrin (β-CD) is commonly used to form inclusion complexes with hydrophobic molecules, improving water solubility and stability upon complexation. Here we report on the mechanochemical synthesis of the inclusion complex β-CD·NP, characterized via a combination of solid-state techniques, including exsitu and in situ X-ray diffraction, Raman and NMR spectroscopies, transmission electron microscopy, and energy dispersive X-ray spectroscopy. The pure inhibitor NP was also structurally characterized. The β-CD·NP complex presents improved solubility and thermal stability, and still inhibits the enzymatic activity of AMO with high efficacy. All results indicate that the inclusion of NP into β-CD represents a viable route for the preparation of a novel class of inhibitors, with improved properties related to stability, water solubility, and good inhibition activity.