The green synthesis of ZnO NPs is becoming increasingly valued for its cost-effectiveness and environmental benefits. This study successfully synthesized hexagonal ZnO NPs using a combination of clove (Syzygium aromaticum) and Thymus capitatus extracts. The use of both extracts significantly improved the antibacterial and antioxidant properties of the ZnO NPs. By optimizing synthesis conditions, including ZnCl2 and extract concentrations, hexagonal wurtzite ZnO NPs were produced at room temperature with only drying at 80 °C without high-temperature annealing. The synthesized ZnO NPs exhibited a hexagonal morphology with an average particle size of 160 nm and a crystallite size of 30 nm. Energy-dispersive X-ray spectroscopy (SEM-EDX) confirmed the elemental composition of the ZnO NPs, showing a high carbon content (63.9 wt.%), reflecting the presence of phytochemicals from the extracts coated the ZnO NPs surface. The UV–Vis spectrum revealed an absorption peak at 370 nm and a bandgap energy of 2.8 eV due to lattice defects caused by organic impurities. The ZnO NPs demonstrated exceptional antioxidant activity, with a DPPH radical scavenging rate of 95.2%. They also exhibited strong antibacterial activity against both Gram-positive and Gram-negative bacteria, with inhibition zones of 25 mm against Bacillus subtilis, 26 mm against Escherichia coli, 24 mm against Salmonella typhimurium, 22 mm against Klebsiella pneumoniae, 21 mm against Staphylococcus aureus, 20 mm against Staphylococcus hominis, and 18 mm against Bacillus subtilis at 200 ppm. Furthermore, significant antifungal activity was observed against Candida albicans, with an inhibition zone of 35 mm at the same concentration. These findings underscore the effectiveness of using combined plant extracts for producing ZnO NPs with controlled morphology and enhanced biological properties, highlighting their potential for various biomedical applications.