Objective To determine antiacanthamoebic activity of natural and marketed honey samples. Methods Natural honey samples were collected directly from the bee hive and marketed honey samples were purchased from the local market in Karachi, Pakistan. Both honey samples were tested for their flavonoid content (quercetin equivalent per gram of the extract) and phenolic content (gallic acid equivalent per gram). Furthermore, their antioxidant activity was determined by measuring 2,2-diphenyl-1-picrylhydrazyl. Using amoebistatic and amoebicidal assays, the effects of honey samples were tested against growth and viability of Acanthamoeba parasites. Results Natural honey exhibited potent amoebistatic and amoebicidal effects, in a concentration-dependent manner. Honey-treated Acanthamoeba castellanii showed loss of acanthopodia, following which amoebae detached, rounded up, reduced in size, decreased in cytoplasmic mass and they were observed floating in the culture medium. Importantly, honey-treated amoebae did not revive when inoculated in fresh growth medium, however, glycerol-treated amoebae exhibited viable trophozoite and active growth. In contrast, marketed honey samples varied in their efficacy against Acanthamoeba castellanii. The proportion of flavonoid, as determined by quercetin measurements and the proportion of phenolic, as determined by gallic acid measurements was higher in natural honey compared with marketed honey. Similarly, the antioxidant activity, as determined by 2,2-diphenyl-1-picrylhydrazyl scavenging activity was higher in natural honey vs. marketed honey. Conclusions This study shows that natural honey has antiacanthamoebic properties and possesses higher flavonoid, phenolic and antioxidant properties compared with the marketed honey. These findings are of concern to the public, health officials, and to the manufacturers regarding production of honey for medical applications.