Antidesma madagascariense Lam. (AM), an indigenous medicinal plant to the Mascarene Islands, is used for the treatment of several diseases. We endeavoured to validate its use via evaluating the kinetics of inhibition of crude aqueous extract (CAE) and crude methanol extract (CME) of AM against key metabolic enzymes (pancreatic lipase, cholesterol esterase [CEase], acetylcholinesterase [AChE], and urease). In vitro antiglycation, antioxidant, cytotoxicity using iCELLigence real time cell analysis system and WST-1 methods, were used. LC–ESI–MS/MS was employed to determine the phenolic composition of the extracts and interaction of selected compounds to the studied enzymes was determined using in silico docking. AChE was inhibited by the CME of AM and CEase by the CAE. Both extracts were active inhibitors of urease and pancreatic lipase. Hyperoside (271.97 μg/g extract), present in large amount in the CME, docked to the enzymatic pocket of urease and CEase. The extracts showed competitive and mixed inhibition of urease and pancreatic lipase, respectively. The antioxidant capacity of the CME (6.61 μg GAE/mg crude extract) was higher compared to CAE (2.20 μg GAE/mg crude extract). AM extracts were significantly (p < 0.05) less potent than aminoguanidine in preventing advanced glycation end products formation. Toxicological screening revealed that both extracts were non-toxic on HEK-293 cells. AM crude extracts at concentrations ranging from 78 to 312 μg/ml did not cause a visible change in cell morphology compared to control. This study supports the safe use of AM as a biomedicine for the management and/or treatment of common non-communicable diseases.