Natural antimicrobials have recently gained increasing interest over synthetic antimicrobials to overcome foodborne pathogens and food microbial contamination. Essential oils (EOs) obtained from resins (BO) were utilized for respiratory disorders, rheumatoid arthritis, malignant tumors, and viral infections. Like other EOs, the therapeutic potential of BO is hindered by its low solubility and bioavailability, poor stability, and high volatility. Several studies have shown excellent physicochemical properties and outstanding therapeutic capabilities of EOs encapsulated into various nanocarriers. This study extracted BO from resins hydrodistillation and encapsulated it into hydroxypropyl-beta-cyclodextrins (HPβCD) using the freeze-drying method. The developed inclusion complexes of BO (BO-ICs) had high encapsulation efficiency (96.79 ± 1.17%) and a polydispersity index of 0.1045 ± 0.0006. BO-ICs showed presumably spherical vesicles (38.5 to 59.9 nm) forming multiple agglomerations (136.9 to 336.8 nm), as determined by UHR-TEM. Also, the formation and stability of BO-ICs were investigated using DSC, FTIR, FE-SEM, UHR-TEM, H NMR, and 2D HNMR (NOESY). BO-ICs showed greater thermal stability (362.7 °C). Moreover, compared to free BO, a remarkable enhancement in the antimicrobial activities of BO-ICs was shown against three different bacteria: , , and . BO-ICs displayed significant antibacterial activity against with an MIC90 of 3.93 mg mL and an MIC50 of 0.57 mg mL. Also, BO-ICs showed an increase in BO activity against with an MIC95 of 3.97 mg mL, compared to free BO, which failed to show an MIC95. Additionally, BO-ICs showed a more significant activity against with an MIC95 of 3.92 mg mL. BO encapsulation showed significantly improved antimicrobial activities owing to the better stability, bioavailability, and penetration ability imparted by encapsulation into HPβCD.