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Abstract Dry beans (Phaseolus vulgarisL.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast‐cooking and slow‐cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant‐seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast‐ and slow‐cooking beans due to soaking. Candidate genes identified in the slow‐cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall‐strengthening enzymes in the slow‐cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.