Staphylococcus aureus causes difficult-to-treat infections with current antibiotics, often linked to resistant biofilms. Honey has the potential to act as an antibiotic due to its acidity and high sugar content. Mechanisms by which honey acts as an antibiotic are unclear. We hypothesize that exposing S. aureus cells to Manuka honey induces physiochemical changes to cells in a concentration-dependent manner. To test our hypotheses, Atomic Force Microscopy (AFM) was used to image cells and quantify their adhesion to a model surface. The Hertz model of contact mechanics was used to estimate the Young’s moduli of the cells. S. aureus was exposed to 10%, 20%, 30% (MIC), and 40% honey for 2 hours. Untreated cells were the negative control. AFM was performed at room temperature on 3 cells per slide, 3 slides per culture, and 3 cultures per condition. Exposure of cells to 10%, 20% and 30% honey for 5 hours resulted in 0%, 45%, and 100% killing of cells, respectively. When cells were untreated, adhesion forces, energies, and elasticities were 17.79±39.72 pN, 4.87±5.06 aJ, and 221.19±100.22 kPa, respectively. Exposure to 10% honey enhanced adhesion forces and energies to 51.41±38.91 pN and 11.86±9.88 aJ, respectively, and did not affect elasticity. Exposure to 20% honey increased adhesion forces and energies further to 102.09±101.04 pN and 14.00±12.91 aJ, respectively, and did not affect elasticity. At 40% honey (above MIC), the adhesion forces and energies reached their maximum values at 356.22±276.98 pN and 81.07±66.37 aJ, respectively, while the elasticity dropped by 70% to 64.32±42.91 kPa. Cells were intact under all conditions investigated. The drop of elasticity could be the result of detachment of surface molecules, while increased adhesion may be associated with increased flexibility of surface molecules. Our results suggest the excellent potential for honey to be used as an antibacterial agent.