In the present study, yellow pea (CDC Amarillo) and faba bean (CDC Snowdrop) seeds were soaked overnight and then germinated in the dark at ambient temperature for 24, 48 and 72 h. During the short-term germination, germination percentages higher than 96.6% were achieved and progressive growth of radicles was observed for both varieties. The soaked and germinated seeds were dried at 55 °C and milled into flours, and their chemical compositions, physicochemical properties and in vitro starch and protein digestibility were systematically examined. Overall, soaking and germination did not noticeably alter the chemical compositions of each flour. The most obvious changes in the physicochemical properties were found in the pasting, emulsifying and foaming properties of the pulse flours. Soaking and 24-h germination greatly enhanced the pasting viscosities of the flours; as the germination proceeded, their viscosities gradually decreased, resulting from the degradation of starch by endogenous amylase(s) during pasting. Germination progressively improved the emulsion activity and stability, foaming capacity and foam stability of both pulse flours. In addition, germination enhanced the in vitro digestibility of starch and protein of the flours; however, the treatment did not improve their in vitro protein digestibility corrected amino acid scores (IV-PDCAAS). Short-term germination of 24-72 h has been demonstrated to be an effective approach to generating pulse flours possessing diverse functional properties and enhanced digestibility of macronutrients.