Stingless bee honey (SBH) contains bioactive compounds which are influenced by its botanical origin, and these constituents are closely associated with its health-promoting properties. Interest in monofloral honey has been increasing owing to its distinctive sensory characteristics and relatively consistent nutritional composition and higher market value. The growing burden of cardiometabolic disease underscores the need for more studies that examine the inhibition of enzymes relevant to these pathways. This study analysed 17 SBH from 13 botanical origins (Acacia, coconut, cocoa, durian, dwarf mountain pine, elderberry, golden shower tree, Mexican creeper, rose myrtle, rubber tree, Singapore rhododendron, starfruit, sunflecks). Thirteen phenolic acids and 21 amino acids were quantified by HPLC. In vitro inhibition was evaluated against enzymes associated with post-prandial glycaemia (α-amylase, α-glucosidase), lipid digestion (pancreatic lipase, cholesterol esterase), cholesterol biosynthesis (HMG-CoA reductase), and blood-pressure regulation (ACE). Elderberry SBH showed the highest ACE inhibition (74.32 ± 0.69%), while Singapore rhododendron SBH exhibited the strongest HMG-CoA reductase inhibition (65.06 ± 1.95%). Sunflecks SBH gave the lowest IC₅₀ for cholesterol esterase (0.57 ± 0.01 µg/mL). PLS regression revealed that gallic acid was the primary contributor to ACE and HMG-CoA reductase inhibition, whereas both gallic acid and rutin were associated with stronger inhibition of digestive lipid-related enzymes. These data show that phenolic and amino-acid profiles differ by botanical origin, and this may help to explain the in vitro enzyme-inhibition patterns of SBH. The findings suggest the potential of SBH as a cardioprotective functional food with significance health benefits.