Developing natural preservatives for wood protection is of great interest in sustainable construction and green building industries. This study was designed to determine the feasibility of using methyl-β-cyclodextrin-essential oils (MβCD-EOs) complexes as potential bio-based preservatives for wood protection. Four essential oils (EOs) with proven antifungal properties, eugenol (EG), trans-cinnamaldehyde (CN), thymol (TM) and carvacrol (CV), were complexed with methyl-β-cyclodextrin (MβCD) by a co-precipitation method. The inclusion of EOs in MβCD and the corresponding inclusion yield of the MβCD-EOs complexes were determined by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and ultraviolet-visible spectroscopy (UV/Vis), respectively. The maximum inclusion yields in MβCD-EG, MβCD-CN, MβCD-CV, and MβCD-TM were estimated to be almost 100%. MβCD-EOs complexes were impregnated into southern pine wood blocks and exposed to two brown rot fungi, Gloeophyllum trabeum and Postia placenta, following procedures described in AWPA Standard E22 and E10. The penetration of MβCD-EOs complexes in wood was confirmed by fluorescence microscopic analysis after the selective dyeing of EOs encapsulated in MβCD. In comparison to the control wood samples, MβCD-EOs complexes treated wood exhibited a significant reduction in the mass loss from 16–36% to 2–18%, accompanied by improvement in radial compression strength loss from 81–92% to 29–67% after four-week fungi exposure. •Methyl-β-cyclodextrin (MβCD) was used as a carrier for antifungal essential oil (EO) compounds.•The inherent instability of EOs was improved through the MβCD encapsulation process.•MβCD-EOs treatment on wood significantly reduces mass and compression strength loss against fungi.•MβCD-EOs complexes show potential for bio-based wood preservatives.