Soil properties in the foraging range of honeybees influence honey composition. We aimed to determine relationships between the antimicrobial properties of New Zealand mānuka (Leptospermum scoparium) honey and elemental concentrations in the honey, plants, and soils. We analyzed soils, plants, and fresh mānuka honey samples from the Wairarapa region of New Zealand for the chemical elements and the antimicrobial activity of the honey as indicated by methylglyoxal (MGO) and dihydroxyacetone (DHA). There were significant negative correlations between honey MGO and the concentrations of Mn, Cu, Mg, S, Na, Ba, K, Zn, and Al. These elements may provide a low-cost means of assessing mānuka honey quality. For individual elements, except for K, there were no correlations between the honeys, plants, and soils. Soil nitrate concentrations were negatively correlated with concentrations of MGO and DHA in the honey, which implies that soil fertility may be a determiner of mānuka honey quality.