Methylated flavonols form a special group with modulating biological activities in comparison with kaempferol and quercetin. The present study isolated ten compounds including two kaempferol methyl ethers: 5-hydroxy-3,7,4′-trimethoxyflavone (1), 3-hydroxy-5,7,4′-trimethoxyflavone (6); four quercetin methyl ethers: retusin (5-hydroxy-3,7,3′,4′-tetramethoxyflavone) (4), 3,5-dihydroxy-7,3′,4′-trimethoxyflavone (5), 3,4′-dihydroxy-5,7,3′-trimethoxyflavone (7), and 3,5,7,3′,4′-pentamethoxyflavone (9); β-sitosterol (2); 5-hydroxy-1-(4′-hydroxyphenyl)eicosan-3-one (3); p-hydroquinone (8); and vanillic acid (10) from the rhizomes and fruit of Amomum koenigii J.F.Gmel. (Zingiberaceae). Their structures were determined by MS, NMR, and X-ray spectroscopic techniques. Among the methylated flavonols, 1, 4–7, and 9 were isolated for the first time from the rhizomes, while 1, 4, and 5 were isolated from the fruit. Compounds 2, 3, 7, 8, and 10 were reported for the first time from the species. Three main methylated flavonols 1, 4, and 5 were quantitatively analyzed in the rhizomes of A. koenigii by RP-HPLC-DAD; their contents were determined to be 1.81% (1), 1.38% (4), and 1.76% (5). The antimicrobial assay against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Aspergillus niger, Fusarium oxysporum, Candida albicans, and Saccharomyces cerevisiae and antioxidant DPPH scavenging test were performed for the isolated methylated flavonols.