This study aimed to compare the phenolic profiles, enzyme inhibitory activity and antioxidant activity of the bulb, stem and flower parts ofAllium paniculatumsubsp.villosulumandAllium paniculatumsubsp.paniculatum. The total phenolic and flavonoid contents of the extracts were spectrophotometrically determined, and the bulb (21.88 mg GAE/g extract) and flower (2.89 mg QE/g extract) parts ofA. paniculatumsubsp.villosulumwere detected with the highest levels. Quantification of selected phenolic compounds was performed using LC-ESI-MS/MS, andp-coumaric acid (981.9, 952.6 mu g/gram extract) was the major compound of both plants. Antioxidant properties of the extracts were evaluated in terms of radical scavenging (DPPH, ABTS) and reducing power (CUPRAC, FRAP) activities, and the highest values were observed in the bulb parts of the plants. Acetylcholinesterase, butyrylcholinesterase and tyrosinase inhibitory activities of the extracts were determined using a 96-well microplate reader. The flower (IC(50)11.72 and 8.43 mu g/ml) and stem parts (IC(50)49.16 mu g/ml) ofA. paniculatumsubsp.villosulumwere the most potent samples. In addition, the results of the analyses were further evaluated and verified by principal component analysis. Conclusively, the variation and correlation of the bioactive compounds and biological activities of the different parts of bothAlliumspecies were investigated with the present research.