The discovery of human induced pluripotent stem cells (hiPSCs) has provided an unprecedented opportunity to study tissue morphogenesis and organ development as “organogenesis-in-a-dish”. Current approaches of cardiac organoid engineering rely on either direct cardiac differentiation from embryoid bodies or generation of aligned cardiac tissues from pre-differentiated cardiomyocytes from monolayer hiPSCs. To experimentally model early cardiac organogenesis in vitro, our protocol combines biomaterials-based cell patterning with stem cell organoid engineering. Three-dimensional cardiac microchambers are created from two-dimensional hiPSC colonies, which approximates an early developing heart with distinct spatial organization and self-assembly. With proper training on photolithography microfabrication, maintenance of human pluripotent stem cells, and cardiac differentiation, a graduate student with guidance will likely be able to carry out this experimental protocol, which requires approximately three weeks. We envisage that this in vitro model of human early heart development could serve as an embryotoxicity screening assay in drug discovery, regulation, and prescription for healthy fetal development. Currently, this protocol has yet to be implemented to assess the cardiac microchamber formation from the hiPSC lines with inherited disease, which can potentially be used to study the disease mechanisms of cardiac malformations at early stage of embryogenesis.