This perspective paper analyses the possibilities and challenges of using cheminformatics as a context for STEM education. The objective is to produce theoretical insights through a SWOT analysis of an authentic educational cheminformatics project where future chemistry teachers engineered a physical 3D model using cheminformatics software and a 3D printer. In this article, engineering is considered as the connective STEM component binding technology (cheminformatics software and databases), science (molecular visualizations), and mathematics (graph theory) together in a pedagogically meaningful whole. The main conclusion of the analysis is that cheminformatics offers great possibilities for STEM education. It is a solution-centered research field that produces concrete artifacts such as visualizations, software, and databases. This is well-suited to STEM education, enabling an engineering-based approach that ensures students' active and creative roles. The main challenge is a high content knowledge demand, derived from the multidisciplinary nature of cheminformatics. This challenge can be solved via training and collaborative learning environment design. Although the work with educational cheminformatics is still in its infancy, it seems a highly promising context for supporting chemistry learning via STEM education.