Fundamental quantum chemistry concepts—quantization of energy, electronic structure, and light–matter interaction—are essential for understanding chemistry and spectroscopy, an important tool for studying molecules. However, very few studies have investigated how students learn and understand these concepts or how their learning can be supported. Drawing on the capacity of writing to support learning of difficult concepts, we designed an intervention that targeted quantum concepts in the context of the use of spectroscopy for identifying chemical composition of the Orion Nebula. A quasi-experimental design with a pre-post assessment on a control and treatment group was used to identify the gains associated with completing the WTL activity. Results from a three-tiered assessment show that WTL students significantly improved in their explanations of the concept of spectroscopic transitions and their overall confidence in their understanding. Analysis of their writing, follow-up interviews, and feedback served to explain the changes observed on the pre-post assessment.