This study examined the effects of Jerusalem artichoke (JA) hot-water extract (JAE) on the quality characteristics of Makgeolli. The purpose was to reduce undesirable discoloration, including browning, that can occur when raw JA is added directly, while enriching Makgeolli with JA-derived soluble nutrients and bioactive compounds. Accordingly, JAE was prepared using the hot-water extract of fresh JA at 0, 5, 10, 15, and 20% (w/w) based on the rice weight. The entire volume of JAE obtained at each level was then added to the Makgeolli mash. The physicochemical properties (color, mineral, free amino acid, and total polyphenol contents), antioxidant activities, and sensory quality were evaluated. The ethanol content (6.08%—6.12%), pH (4.02—4.07), and titratable acidity (0.18%—0.24%) were similar across treatments. By contrast, the soluble solids (°Brix) increased slightly from 3.1% in the control to 3.4%—4.2% in the JAE-added samples. In proportion to the addition of JAE, the L* values of the Hunter color decreased from 52.37 to 40.00; the a* values increased from —0.32 to 3.21, and the b* values showed the largest rise. The K and Ca levels were 120.11—145.11 mg/L, Zn decreased from 80.29 to 32.00—35.18 mg/L, while the Fe and Mg levels increased, reaching 89.71 mg/L and 79.77 mg/L at 20% JAE. The Mn and Cu contents remained stable, and no toxic heavy metals (As, Hg, Cd, and Pb) were detected. The essential amino acids levels followed the order, Phe > Lys > Trp > Val > Ile > Met > Thr > Leu > His, and the key free amino acids (Ala, Glu, and Arg) and functional amino acids, such as L-ornithine, γ-aminobutyric acid, increased in proportion with JAE addition. The total polyphenol content increased from 312.11 mg% to 326.23—404.31 mg%, enhancing the DPPH and hydroxyl radical scavenging activities. The sensory evaluation indicated significantly higher scores in taste, color, aroma, and overall acceptability for Makgeolli with 5%—20% JAE compared to the control. Thus, JAE addition can simultaneously enhance the nutritional, functional, and sensory qualities of Makgeolli, supporting its potential as a functional fermented beverage. The optimal percentage JAE addition, as determined by sensory scoring, was approximately 15%.