Research has demonstrated that simulation-based inquiry learning has significant advantages for learning outcomes when properly scaffolded. For successful learning in science with simulation-based inquiry, one needs to ascertain levels of background knowledge so as to support learners in making, evaluating and modifying hypotheses, conducting experiments and interpreting data, and to regulate the learning process. This case study examines the influence of scaffolded simulation-based inquiry learning on fifth-graders' (n?=?21) models of the greenhouse effect. The pupils were asked to make annotated drawings about the greenhouse effect both before and after scaffolding through simulation-based instructional interventions. The data were analysed qualitatively to investigate the impact of the interventions on the representations that pupils used in their descriptions of the greenhouse effect. It was found that scaffolded simulation-based inquiry learning noticeably enriched the concepts pupils used in their representations leading to better understanding of the phenomenon. In many cases, the fifth graders produced quite sophisticated representations.