Advances in treating β cell loss include islet replacement therapies or increasing cell proliferation rate in type 1 and type 2 diabetes. We previously developed a proliferation-inducing prodrug (ZnPD6) that targets the high concentration of zinc ions in β cells, and which exhibits a 2.4-fold increase in β cell proliferation compared to the DYRK1A inhibitor harmine. These prodrugs were identified through screening on the Disque Platform (DP)—a high-fidelity culture system where stem cell–derived β cells are reaggregated into thin, 3D discs within 2D 96-well plates that mimic in vivo conditions. The Disque Platform allows for the formation of 3D micro-tissues within an automation-friendly design, and is capable of systematically manipulating the cell niche in order to identify chemical and physical cues that enhance β cell proliferation. The Disque Platform better replicates the zinc content of native islets, enabling for the screening of zinc-activated prodrugs whose activity cannot be detected in 2D culture systems, which typically display a markedly lowered zinc content. The Disque Platform is a reliable screening platform that bridges the advantages of 2D and 3D culture systems and responds to interventions when conventional systems cannot produce a clear signal or readout. Here we describe a standard protocol for the formation of 3D micro-tissues in the Disque Platform.