•PLGA microspheres based on exenatide encapsulated in nanoparticles were developed.•Ex-NPs-PLGA-Ms was prepared by modified S/O/W method with a low initial burst.•Ex-NPs-PLGA-Ms achieved zero-order controlled release.•S/O/W method could preserve the bioactivity of exenatide without cytotoxicity. This study aimed to prepare poly (D, L-lactic-co-glycolic acid) microspheres (PLGA-Ms) by a modified solid-in-oil-in-water (S/O/W) multi-emulsion technique in order to achieve sustained release with reduced initial burst and maintain efficient drug concentration for a prolonged period of time. Composite PLGA microspheres containing exenatide-encapsulated lecithin nanoparticles (Ex-NPs-PLGA-Ms) were obtained by initial fabrication of exenatide-loaded lecithin nanoparticles (Ex-NPs) via the alcohol injection method, followed by encapsulation of Ex-NPs into PLGA microspheres. Compared to Ms prepared by the conventional water-in-oil-in-water (W/O/W) technique (Ex-PLGA-Ms), Ex-NPs-PLGA-Ms showed a more uniform particle size distribution, reduced initial burst release, and sustained release for over 60 d in vitro. Cytotoxicity studies showed that Ms prepared by both techniques had superior biocompatibility without causing any detectable cytotoxicity. In pharmacokinetic studies, the effective drug concentration was maintained for over 30 d following a single subcutaneous injection of two types of Ms formulation in rats, potentially prolonging the therapeutic action of Ex. In addition, administration of Ex-NPs-PLGA-Ms resulted in a more smooth plasma concentration-time profile with a higher area under the curve (AUC) compared to that of Ex-PLGA-Ms. Overall, Ex-NPs-PLGA-Ms prepared by the novel S/O/W method could be a promising sustained drug release system with reduced initial burst release and prolonged therapeutic efficacy. Display omitted