Research on the effectiveness of immersive VR for science learning has found mixed results when VR learning is compared to traditional learning. While media comparison studies have been criticised for their methodological problems, they provide important information for policy makers as well as for educators. We believe the mixed results were found because many VR learning environments do not take advantage of the unique affordances of VR. We therefore designed Looking Inside Cells (LIC), a set of VR simulations that are interactive, immersive, use spatial features of VR, and take advantage of emotional design. We compared LIC to a slide show of the same content in a quasi-experimental between-subject control group design (N = 63). Outcome variables were recall, comprehension, interest, motivation, and experienced emotions. Results indicate that learners in the VR group scored significantly higher than learners in the control group on some dimensions of the post assessment. The treatment group reported higher levels of positive affect and interest. The results endorse the idea that adopting an affordances approach can enhance the effectiveness of VR in a learning context.