Methanolic extracts of Moltkia aurea Boiss. (MA) and Moltkia coerulea (Willd.) Lehm. (MC) were investigated for their antioxidant capacity and enzymatic inhibitory potential against acetylcholinesterase, butyrylcholinesterase, α-amylase, α-glucosidase, and tyrosinase in vitro. MA and MC were also explored for their antimicrobial effect, as well as for their possible genotoxic/antigenotoxic potential on Drosophila melanogaster in vivo. The total bioactive components (phenolic (TPC) and flavonoid contents (TFC)) were determined and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolite profiling of MA and MC appraised. The plausible docking poses of bioactive compounds to key enzymes were further studied using molecular modelling approach. MA proved to be a better antioxidant with higher TPC and TFC compared to MC. Protocatechuic acid, rutin, hesperidin and malic acid were the most abundant in these extracts. Both MA and MC exhibited antigenotoxic potential with a %R in DNA damage of 60.90 and 53.14% respectively. The docking studies revealed that rutin, hesperidin, and rosmarinic acid have the best scores for all the enzymes tested. MA and MC were found to be rich in phytochemicals with potent antioxidant, antimicrobial, and antigenotoxic activities that can be further studied for the management of neurodegenerative complications, diabetes, and hyperpigmentation.