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Antimicrobial resistance has posed considerable health and economic burdens globally (approximately five million deaths annually), particularly in developing countries. The estimated annual treatment costs in the United States include US$4.6 billion. Vast antibiotic resistance among Gram-negative and Gram-positive bacterial species has spread from healthcare to the environment, community, and animals. These conditions have limited and in some cases, failed infection eradication options and facilitated the distribution of drug-resistant organisms. The spread of drug-resistant bacterial infections is a major human health concern, hence, seeking novel antibacterial agents is crucial. This study used nanoemulsions of Citrus aurantium and Artemisia annua essential oils (EOs) as natural antibacterial agents. Gas chromatography mass spectrometry (GC-MS) analysis showed that limonene (31.4%) and artemisia ketone (26.2%) were major components, respectively. After that, their nanoemulsion dosage forms with mean droplet sizes of 181 ± 7 and 160 ± 5 and zeta potential values 3.1 ± 0.8 and -4.9 ± 0.5 mV were prepared. Meanwhile, successful loading of the EOs in nanoemulsion was confirmed by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) analysis. A. annua nanoemulsion with 40% antioxidant effect was significantly more potent than C. aurantium nanoemulsion. Meanwhile, nanoemulsions' antibacterial and antibiofilm activity against clinical and standard strains, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumonia, were investigated. The best efficiency was related to the effect of C. aurantium nanoemulsion against S. aureus; minimum inhibitory (MIC) and minimum bactericidal concentrations (MBC) were 500 and > 2000 µg/mL. In addition, no biofilm was formed after treatment with both nanoemulsions. Therefore, C. aurantium and A. annua EO nanoemulsions may act as natural antioxidant and antibacterial agents in complementary medicine.