The stingless bee Heterotrigona itama honey is generating interest among consumers due to unique antibacterial properties. Despite the substantial health benefits of this honey, its action mode of inhibiting and killing pathogenic bacteria remains unresolved. The present study aimed to unravel the effect of raw H. itama honey against four clinically important bacteria, Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. Total phenolic and total flavonoid contents, alongside antioxidant and antibacterial activities of honey samples were established to identify the 'best' raw honey. Honey Sy-1 showing the highest amount of phenolics (80.71 mg GAE/100 g) and antioxidant capacity (82.67%) and, the lowest MIC (1.56% (w/v)) and MBC (3.125% (w/v)), was tested against four bacterial cells, wherein any alterations in cellular morphology were observed under scanning electron microscope. The micrographs revealed significant elongation/filamentation in B. subtilis cells, de-flagellation in P. aeruginosa, membrane perturbation and leakage of intracellular contents in E. coli alongside non-dividing septated cells in S. aureus. H. itama honey inhibited bacterial growth by disrupting the cell membrane in conjunction to interacting with a cytosolic target or possibly interrupted septum formation and blocking DNA and protein syntheses. The evidence strongly supported the natural antibacterial properties of the H. itama honey.