In the present study, we report the in-vitro antifungal activity of ZnO nanoparticles (NPs) against three species of the ambrosia beetle mutualistic fungi, Raffaelea arxii, Raffaelea subfusca, Raffaelea lauricola. The latter is the causal agent of laurel wilt, a deadly vascular disease of avocado. The effect of coating and size of two kinds of ZnO-NPs on the antifungal activity against those mutualistic is presented. The NPs obtained by the hydrothermal method (hyd-ZnO) were uncoated plate-like NPs with sizes between 200 and 600 nm, while the NPs obtained by sol–gel (sg-ZnO) were PEG-coated semi-spherical NPs with ~60 nm in size. Although the inhibition percentage was higher than 80% for both kinds of NPs (at a concentration of 0.5 mg/ml), the highest antifungal capacity was exhibited by the hyd-ZnO-NPs. Here we show that despite the size of the NPs, which is a crucial parameter, the coating of ZnO-NPs is the most critical factor for the improvement of their antifungal properties.