One of the major disadvantages associated with macromolecules therapy is that most of them can only be administered parenterally. Exenatide, an efficient anti-diabetic drug, incretin mimetic, is currently administered subcutaneously (SC) causing compliance issues. Nanoparticles (NPs) are considered a promising solution for oral delivery of this drug. In order to overcome exenatide's inability to cross the enterocytes and to increase its stability in the gastrointestinal (GI) tract, we encapsulated exenatide into a nano-in-micro delivery system. This drug delivery system (DDS) improved the relative oral bioavailability of exenatide, in comparison to Byetta® injection SC. In this study, we report about the efficacy of this DDS to improve glycemic parameters in diabetic ob/ob mice. Our results suggested that our DDS successfully lowered blood glucose levels (BGL) raised insulin levels, decreased glycated hemoglobin and maintained the body weight of the mice. These findings validate the efficacy of this DDS in promoting oral delivery of exenatide and will hopefully improve patient compliance and adherence. The potential of this DDS to encapsulate other leading peptides and proteins, such as insulin, was also evaluated in this study. It was found that peptides up to 6 kDa can be efficiently encapsulated, but the in-vivo performance is also dependent on other physicochemical properties.