Islet microencapsulation is a promising solution to diabetes treatment, but its quality control based on manual microscopic inspection is extremely low-throughput, highly variable, and laborious. This study presents a high-throughput islet-encapsulation quality screening system based on lens-free on-chip imaging with a wide field-of-view of 18.15 cm2, which is more than 100× larger than that of a lens-based optical microscope, enabling it to image and analyze ∼8000 microcapsules in a single frame. Custom-written image reconstruction and processing software provides the user with clinically important information, such as microcapsule count, size, intactness, and information on whether each capsule contains an islet. This high-throughput and cost-effective platform can be useful for researchers to develop better encapsulation protocols as well as perform quality control prior to transplantation.