The number of patients with diabetes mellitus is increasing at an alarming rate and this situation has triggered the interest of searching natural product as an alternative treatment. Stingless bee honey containing a diverse array of bioactive compounds is commonly utilized as a functional food and also found to possess various therapeutic effects including anti-diabetic through α-amylase and α-glucosidase inhibition. However, the composition level of bioactive compounds varying of geographical origins and botanical sources of honey leads to different enzyme inhibition abilities. Therefore, this study explored the total phenolic, total flavonoid, α-amylase and α-glucosidase inhibition activities of stingless bee honey from various botanical origins. In this study, stingless bee honey was collected from 6 different botanical origins namely, acacia, coconut, mangrove, starfruit, multifruit and multiflower plant. Honey from tualang tree was used as a positive control. Phenolic and flavonoid contents as well as α-amylase and α-glucosidase inhibition activities of honey were studied spectrophotometrically. Stingless bee honey from mangrove was found to have the highest phenolic content (141.74±0.03 mg GAE/100 g). The honey collected from coconut origin showed the highest flavonoid content with the value of 51.33±0.02 mg RE/100 g and also achieved the highest percentage inhibition against α-glucosidase (68.33% at 100 µg/mL). Furthermore, tualang honey and honey samples from mangrove, coconut and Acacia tree were found to have strong α-amylase inhibition abilities as their inhibition percentages were more than 70.00% at 100 µg/mL. This study showed that the presence of flavonoid and phenolic compounds in honey from different botanical origins yielded different degree of α-amylase and α-glucosidase inhibition and also recommended the uses of stingless bee honey in diabetes treatment.