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Abstract The stability, sensitivity, and volatility of essential oils are some of their most serious limitations, and nanoencapsulation has been considered one of the most effective techniques for solving these problems. This research aimed to investigate the incorporation of Salvia rosmarinus Speen and Cedrus atlantica Manetti (MEO) essential oil mixture in Gum Arabic (GA) and to evaluate nanoencapsulation’s ability to promote antifungal activity against two brown rot fungi responsible for wood decay Gloeophyllum trabeum and Poria placenta. The optimization of encapsulation efficiency was performed using response surface methodology (RSM) with two parameters: solid-to-solid (MEO/GA ratio) and solid-to-liquid (MEO/ethanol). The recovered powder characterization was followed by various techniques using a scanning electron microscope (SEM), X-ray diffractometry (XRD), dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR), and thermo-gravimetric analysis (TGA). The optimal nanoencapsulating conditions obtained from RSM were ratios of MEO/GA of 1:10 (w/w) and MEO/ethanol of 10% (v/v), which provided the greatest encapsulation efficiency (87%). The results of SEM, XRD, DLS, FTIR, and TGA showed that the encapsulation of MEO using GA modified particle form and molecular structure and increased thermal stability. An antifungal activity assay indicated that an effective concentration of MEO had an inhibitory effect on brown rot fungi. It had 50% of the maximal effect (EC50) value of 5.15 ± 0.88 µg/mL and 12.63 ± 0.65 µg/mL for G. trabeum and P. placenta, respectively. Therefore, this product has a great potential as a natural wood preservative for sustainable construction and green building.