Functional foods containing peptides offer the possibility to modulate the absorption of sugars and insulin levels to prevent diabetes. This study investigates the potential of germinated soybean peptides to modulate postprandial glycaemic response through inhibition of dipeptidyl peptidase IV (DPP-IV), salivary α-amylase, and intestinal α-glucosidases. A protein isolate from soybean sprouts was digested by pepsin and pancreatin. Protein digest and peptide fractions obtained by ultrafiltration (<5, 5–10 and >10 kDa) and subsequent semipreparative reverse phase liquid chromatography (F1, F2, F3, and F4) were screened for in vitro inhibition of DPP-IV, α-amylase, maltase, and sucrase activities. Protein digest inhibited DPP-IV (IC50 = 1.49 mg/mL), α-amylase (IC50 = 1.70 mg/mL), maltase, and sucrase activities of α-glucosidases (IC50 = 3.73 and 2.90 mg/mL, respectively). Peptides of 5–10 and >10 kDa were more effective at inhibiting DPP-IV (IC50 = 0.91 and 1.18 mg/mL, respectively), while peptides of 5–10 and <5 kDa showed a higher potency to inhibit α-amylase and α-glucosidases. Peptides in F1, F2, and F3 were mainly fragments from β-conglycinin, glycinin, and P34 thiol protease. The analysis of structural features of peptides in F1–F3 allowed the tentative identification of potential antidiabetic peptides. Germinated soybean protein showed a promising potential to be used as a nutraceutical or functional ingredient for diabetes prevention.