Despite its high cost, the success rate for in vitro fertilization (IVF) remains < 33% in humans, driving the need for new techniques to improve embryo culture outcomes. The well-of-the-well (WOW) culture system is a platform for in-vitro mammalian embryo culture that has been shown to enhance the developmental competence of embryos and clinical pregnancy rates in humans. However, discovery and testing of the best design for optimal embryo culture quality is hindered by the lack of a method to flexibly produce WOW dishes of various designs. Here, we present a low-cost and simple method to fabricate WOW dishes with microwells of arbitrary shapes and dimensions. We use a low-cost 3D printing service to fabricate a poly(dimethylsiloxane) (PDMS)-based WOW insert that can be paired with a standard in vitro fertilization (IVF) dish to create WOW dishes with new microwell shapes, including pyramidal and hemispherical designs. We validate the fabrication quality of the WOW inserts and demonstrate the utility of the assembled WOW dishes for observation and grading of mouse embryo quality. Moreover, our results indicate that WOW dishes with hemispherical microwells result in better culture outcomes than traditional flat-bottomed IVF dishes and those with other microwell shapes, including the semi-elliptical microwells used in commercial WOW dishes. The proposed fabrication strategy thus provides a way to rapidly fabricate and test new WOW dishes that may bolster IVF success rates.