Green honey is exclusively available on the island of Banggi in Sabah, and its uniqueness sees the commodity being sold at a high market price. Therefore, green honey is prone to adulteration by unscrupulous individuals, possibly compromising the health of those consuming this food commodity for its curative properties. Moreover, an established standard for reducing sugar in green honey is unavailable. Ipso facto, the study aimed to profile green honey’s physical and chemical properties, such as its pH, moisture content, free acidity, ash content, electroconductivity, hydroxymethylfurfural (HMF), total phenolic content, total flavonoid content, DPPH, colour, total sugar content, total protein content, and heavy metals as well as volatile organic compounds, the data of which are profoundly valuable in safeguarding consumers’ safety while providing information for its quality certification for local consumption and export. The results revealed that the honey’s physicochemical profile is comparable to other reported kinds of honey. The honey’s naturally green colour is because of the chlorophyll from the nectar from various flowers on the island. The raw honey showed free acidity between 28 and 33 Meq/100 g, lower than the standard’s 50 Meq/100 g. The hydroxymethylfurfural content is the lowest compared to other reported honey samples, with the total phenolic content between 16 and 19 mg GAE/100 g. The honey’s reducing sugar content is lower (~37.9%) than processed ones (56.3%) because of water removal. The protein content ranged from 1 to 2 gm/kg, 4- to 6-fold and 2-fold higher than local and manuka honey, respectively. The exceptionally high content of trans-4-hydroxyproline in raw honey is its source of collagen and other healing agents. Interestingly, low levels of arsenic, lead, nickel, cadmium, copper, and cobalt were detected in the honey samples, presumably due to their subterranean hives. Nevertheless, the honey is fit for general consumption as the concentrations were below the maxima in the Codex Alimentarius Commission of 2001.