The present investigation aimed to develop inclusion complexes (ICs) from Psidium gaudichaudianum (GAU) essential oil (EO) and its major compound β-caryophyllene (β-CAR), and to evaluate their herbicidal (against Lolium multiflorum and Bidens pilosa) and cytogenotoxic (on Lactuca sativa) activities. The ICs were obtained using 2-hydroxypropyl-β-cyclodextrin (HPβCD) and they were prepared to avoid or reduce the volatility and degradation of GAU EO and β-CAR. The ICs obtained showed a complexation efficiency of 91.5 and 83.9% for GAU EO and β-CAR, respectively. The IC of GAU EO at a concentration of 3000 µg mLsup.−1 displayed a significant effect against weed species B. pilosa and L. multiflorum. However, the β-CAR IC at a concentration of 3000 µg mLsup.−1 was effective only on L. multiflorum. In addition, the cytogenotoxic activity evaluation revealed that there was a reduction in the mitotic index and an increase in chromosomal abnormalities. The produced ICs were able to protect the EO and β-CAR from volatility and degradation, with a high thermal stability, and they also enabled the solubilization of the EO and β-CAR in water without the addition of an organic solvent. Therefore, it is possible to indicate the obtained products as potential candidates for commercial exploration since the ICs allow the complexed EO to exhibit a more stable chemical constitution than pure EO under storage conditions.