Tofu, a widely consumed soy-based product, has seen increasing consumer demand, driven by health and dietary trends. Enhancing the processing suitability of soybeans requires analysis of the genetics associated with tofu quality traits. In this study, five key traits, namely water absorption (WA%), Brix of soymilk (°BS), soymilk yield (YM%), tofu residue (TR%), and tofu yield (YT%), were evaluated in two recombinant inbred line (RIL) populations: 81 lines of “Daepung”דSaedanbaek” and 122 lines of “Daepung”דGalchae”. Most traits exhibited normal distributions and transgressive segregation. Trait correlations revealed strong associations between WA and TR, and between YM and YT, with population-specific variation. Quantitative trait locus (QTL) mapping identified eight loci in each population linked to WA, °BS, YM, TR, and YT across multiple chromosomes. Notably, co-localized QTL were detected for WA% and TR% (chromosomes 1 and 6) and for WA%, YM%, °Brix, and TR% (chromosome 8), indicating pleiotropic regulation. Candidate genes included Glyma.06g173500, associated with β-glucan biosynthesis, and Glyma.03g132700, encoding β-glucanase, both implicated in seed coat permeability and tofu yield. These results provide novel genetic insights into seed coat properties and processing quality, and the identified QTLs and candidate genes represent valuable targets for marker-assisted selection in soybean breeding programs optimized for tofu production in Korea.