This study investigated the influence of chitosan (CH) and hydroxypropyl methylcellulose (H), along with ultrasound power, on the physicochemical properties, antifungal activity, and stability of oil-in-water (O/W) nanoemulsions containing thymol and cinnamaldehyde in a 7:3 (v/v) ratio. Eight O/W formulations were prepared using CH, H, and a 1:1 (v/v) blend of CH and H, both with and without ultrasonication (U). Compared to untreated samples, U-treated nanoemulsions had lower droplet sizes (433-301 nm), polydispersity index (0.42-0.47), and zeta potential (-0.42-0.77 mV). The U treatment decreased L* and b* values, increased a* color attribute values, and increased apparent viscosity (0.26-2.17) at the same shear rate. After 28 days, microbiological testing of nanoemulsions treated with U showed counts below the detection limits (< 2 log CFU mL-1). The U-treated nanoemulsions exhibited stronger antifungal effects against R. stolonifer, with the NE/CH-U and NE/CH-H-U formulations demonstrating the lowest minimum inhibitory and fungicidal concentrations, measured at 0.12 and 0.24 μL/mL, respectively. On day 28, U-treated nanoemulsions demonstrated higher ionic, thermal, and physical stability than untreated samples. These findings suggest that the stability and antifungal efficacy of polysaccharide-based nanoemulsions may be improved by ultrasonic treatment. This study paves the way for innovative, highly stable nanoemulsions.