Allium (A.) species are one of the most widespread plants in the world, which have played a special role in terms of nutrition, treatment, and economy since long ago. This study is the first report on the phytochemical and biological activities of A. colchicifolium. Five flavonoids, including isorhamnetin (compound 1), quercetin (compound 2), morin (compound 3), isorhamnetin-3-O-glucoside (compound 4), and quercetin 3-O-glucoside (compound 5), were isolated and purified for the first time from A. colchicifolium leaves. All isolated flavonoids showed antibacterial and antibiofilm activities. Compound 3 revealed prominent antibacterial activities against Staphylococcus (S.) aureus and Proteus (P.) mirabilis. Also, compounds 3 and 5 showed the highest antibiofilm activities on S. aureus and P. mirabilis, respectively. The docking study results showed that compounds 3, 4, and 5 had the most robust interactions with two critical proteins in biofilm formation, including staphylococcal accessory regulator A (SarA) and mannose-resistant Proteus-like fimbriae H (MrpH). Besides, compounds 2 and 3 revealed significant antioxidant activities in 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and ferric (Fe3+)-reducing antioxidant power (FRAP) tests compared to the other compounds and positive controls. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) prediction assay showed that compounds 1, 2, and 3 have suitable physicochemical and pharmacokinetic properties. The results of this study confirm that the flavonoids isolated from the leaves of A. colchicifolium can be promising candidates for use in the pharmaceutical and food industries.