Antibiotic resistance is one of the most important public health concerns worldwide. Essential oils especially as micro- and nanoemulsion formulations are emerging as potential agents to target resistant pathogens and as drug delivery vehicles. Cinnamon and clove oils were formulated into nanoemulsions using Brij 35 or Tween 20. Based on the physicochemical characteristics and stability, CiB-3, ClB-3, CiT20-5 and ClT20-5 were identified as optimised emulsions and their anti-Staphylococcal properties were determined. Hydrodynamic diameter of the oil droplets was < 15 nm. The emulsions have only 5% of oil, and there was an 83–166-fold improvement in static MIC over the bulk oil. Inocula ranging from 105 to 107 CFU mL−1 of both MSSA and VISA strains did not significantly affect the activity of all four nanoemulsions. Tween 20 containing nanoemulsions had higher anti-biofilm activity (66–76%) and the activity was comparable between MSSA and VISA. ClT20-5 decreased the viable counts of both strains below detectable limits by 24 h. There was a statistically significant difference in leakage of 260-nm-absorbing cellular components between MSSA and VISA at 30 min (CiB-3: P = 4.67e−013, ClB-3: P = 2.49e−010, CiT20-5: P = 0.00028, ClT20-5: P = 0.00056) and at 60 min (CiB-3: P = 1.37e−014, ClB-3: P = 4.14e−014, CiT20-5: P = 5.30e−012, ClT20-5: P = 2.82e−009). The SEM images of the treated and untreated cells show significant damage and alteration in the morphology of the emulsion treated cells. This study demonstrates the significant anti-Staphylococcal activity of cinnamon and clove oil against MSSA and VISA strains. © 2019, King Abdulaziz City for Science and Technology.