Syzygium aromaticum (L.) Merr. & L.M. Perry is a known spice with a high phytochemical content that can be explored in drug discovery. We investigated the in vitro enzyme inhibitory activities of a flavonoid-rich extract of S. aromaticum (FRESA) against type II diabetes (T2D) and Alzheimer’s disease (AD) and identified its anti-T2D and anti-AD phytochemicals via computational prediction. The in vitro enzyme inhibitory activities of a flavonoid-rich extract of Syzygium aromaticum were evaluated via standard protocols following flavonoid-enriched extraction procedures. High-performance liquid chromatography (HPLC) was employed to characterize the constituent bioactive flavonoids. Molecular docking of eight phytochemicals was performed via AutoDock Vina in PyRx 0.8, which identified apigenin, myricetin, and quercetin as hit compounds with high binding affinities and multitarget activities against α-amylase, α-glucosidase, acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and monoamine oxidase (MAO). Molecular dynamics simulations (100 ns) were conducted via GROMACS 2019.2, and binding free energy calculations were performed via the MM-GBSA approach to validate the stability and interaction integrity of the hit phytochemicals. FRESA (IC₅₀ = 961.943 ± 21.031 μg/mL) exhibited moderate activity against α-amylase compared with that of acarbose (IC₅₀ = 27.104 ± 0.270 μg/mL). Compared with acarbose (IC₅₀ = 17.389 ± 0.436 μg/mL), FRESA had appreciable activity against α-glucosidase (IC₅₀ = 562.045 ± 6.714 μg/mL). FRESA demonstrated significant (p < 0.0001) inhibition of acetylcholinesterase (IC₅₀ = 26.911 ± 0.058 µg/mL), surpassed galantamine (IC₅₀ = 27.950 ± 0.122 µg/mL), and moderately inhibited butyrylcholinesterase (IC₅₀ = 28.168 ± 0.702 µg/mL) to galantamine (IC₅₀ = 23.126 ± 0.683 µg/mL). FRESA also significantly suppressed monoamine oxidase activity in Fe²⁺-induced brain damage in a concentration-dependent manner. HPLC–DAD analysis identified apigenin, caffeic acid, ferulic acid, gallic acid, kaempferol, myricetin, quercetin, and syringic acid as major constituents. Molecular docking revealed apigenin, myricetin, and quercetin as top-ranked multitarget inhibitors, exhibiting strong binding affinities (− 9.0 to − 10.2 kcal/mol) comparable to those of reference inhibitors across α-amylase, α-glucosidase, AChE, BChE, and MAO. Molecular dynamics simulations and MM-GBSA confirmed the binding strength of the hit phytoconstituents in the active pockets of α-amylase, α-glucosidase, AChE, BChE, and MAO, with multitargeting inhibitory activities supporting the in vitro and ex vivo enzyme activities. ADMET profiling indicated favorable drug likeness for apigenin, whereas myricetin and quercetin displayed acceptable pharmacokinetic properties with minimal violations. Our findings provide scientific validation of the anti-T2D and anti-AD properties of S. aromaticum and identify apigenin, myricetin, and quercetin, which could be used for the development of inhibitors of α-amylase, α-glucosidase, AChE, BChE, and MAO as dual therapies to combat T2D and AD. Additional in vivo validation is recommended to ensure a thorough assessment in the present research.