Dataset documenting peptide profile in the spermosphere of germinating common bean (Phaseolus vulgaris L.) seeds. In this study we assessed the composition of seed exuded peptides in the spermosphere and how exuded peptides are influenced by both the location of seed production and the genetic background. One seed lot corresponds to seeds from one genotype produced in one location. Three independent biological replicates were conducted for each seed lot. Thus, 48 samples were analysed, corresponding to three replicates of eight genotypes produced in two locations. Spermosphere collection of germinating seeds involved the imbibition of 30 seeds for each sample at four distinct time intervals: 2, 8, 16, and 24 hours. The collected spermosphere, consisting of the water surrounding germinating seeds, was gathered for each time interval and subsequently pooled and analysed by an untargeted LC-MS/MS peptidomic approach.