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Abstract BackgroundChi and colleagues have argued that some of the most challenging engineering concepts exhibit properties of emergent systems. However, students often lack a mental framework, or schema, for understanding emergence. Slotta and Chi posited that helping students develop a schema for emergent systems, referred to as schema training, would increase the understanding of challenging concepts exhibiting emergent properties. PurposeWe tested the effectiveness of schema training and explored the nature of challenging concepts from thermodynamics and heat transfer. We investigated if schema training could (a) repair misconceptions in advanced engineering students and (b) prevent them in beginning engineering students. MethodWe adapted Slotta and Chi's schema training modules and tested their impact in two studies that employed an experimental design. Items from the Thermal and Transport Concept Inventory and expert‐developed multiple‐choice questions were used to evaluate conceptual understanding of the participants. The language used by students in their open‐ended explanations of multiple‐choice questions was also coded. ResultsIn both studies, students in the experimental groups showed larger gains in their understanding of some concepts—specifically in dye diffusion and microfluidics in Study One, and in the final test for thermodynamics in Study Two. But in neither study did students exhibit any gain in conceptual questions about heat transfer. ConclusionOur studies suggest the importance of examining the nature of the phenomena underlying the concepts being taught because the language used in instruction has implications for how students understand them. Therefore, we suggest that instructors reflect on their own understanding of the concepts.