This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein–chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant–pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.