Type 2 diabetes mellitus (T2DM) is a leading cause of death globally. T2DM patients experience glucose intolerance, and inhibitors of dipeptidyl peptidase IV (DPP-IV) and α-glucosidase are used as drugs for T2DM management. DPP-IV and α-glucosidase inhibitors are also naturally contained in foods, but their potency can be affected by the food matrix and processing methods. In this study, germination and solid-state fermentation (SSF) were used to alter pulse seed microstructures, to convert compounds into more bioactive forms, and to improve their bioaccessibility. Germination substantially modified the seed microstructure, protein digestibility, contents and profiles of phenolic compounds in all the pulses. It also increased DPP-IV and α-glucosidase inhibitory activities in chickpeas, faba beans and yellow peas. Compared to germination, SSF with Lactobacillus plantarum changed the content and the profile of phenolic compounds mainly in yellow peas and green lentils because of greater disruption of the seed cell wall. In the same pulses, heat treatment and SSF of flour increased DPP-IV and α-glucosidase inhibitory activities. The results of this study suggest that germination and SSF with L. plantarum are effective and simple methods for modulating phenolic and protein profiles of common pulses and improve the action on DPP-IV and α-glucosidase.