This study investigated the fermentation and quality characteristics of Makgeolli produced from different wheat cultivars using Saccharomyces cerevisiae Y263 yeast. The wheat cultivars used for brewing analysis were imported wheat (IW), Geumgang (GG), Wooju (WJ), Saegeumgang (SGG), Hojoong (HJ), Baekchal (BC), Joa (JA), Goso (GS), Baekgang (BG), Jogyung (JG), Arijinheuk (ARJH), Hwanggeumal (HGA), and Jeonju-432ho (JJ-432). Among the raw wheat flour varieties, IW and SGG had the highest carbohydrate content, while HGA had the highest protein content. The fermentation results showed that the low amylose BC exhibited faster CO₂ production. The alcohol content ranged from 13.97% to 17.67%, with HGA Makgeolli showing the lowest value and the highest total acid (1.41%) and volatile acid (791.93 mg/L) contents. The volatile acid content was higher in the Makgeolli made from HGA. By contrast, BC and SGG Makgeolli exhibited a higher sugar content. Organic acid analysis showed that lactic and acetic acids dominated the acid profile, and high lactic and acetic acids levels in HGA Makgeolli. Free amino acid analysis revealed leucine and phenylalanine as the dominant bitter-tasting amino acids, with the highest levels in HGA and the lowest in BC Makgeolli. Volatile aroma compounds, analyzed using an electronic nose and confirmed by discriminant function analysis, identified ethyl acetate, ethyl octanoate, and ethyl hexanoate as the key contributors to the sweet and fruity notes differentiating the samples. The sensory evaluation using the Rate-All-That-Apply (RATA) showed that the Makgeolli made from SGG and BC had higher scores in flavor and overall acceptability, associated with a nutty flavor, umami, sweetness, and yogurt flavor, whereas HGA was perceived as having viscosity and Chalky mouthfeel with a low preference. Overall, this study provides comprehensive insights into the influence of wheat cultivar differences on physicochemical, sensory, and aromatic properties of wheat Makgeolli, offering a foundation for the development of optimized brewing using domestic wheat varieties.