<p>The incorporation of metacognitive scaffolding into science education may foster self-regulated learning, potentially leading to significant improvements in student outcomes. Accordingly, this study investigates the effects of embedding metacognitive scaffolding within a PhET (Physics Education Technology) interactive simulation to enhance elementary school students’ conceptual understanding of force and motion. Fifty-four sixth-grade students from two classes were randomly allocated to either an experimental group which engaged with a physics simulation augmented by computer-based metacognitive scaffolding, or a control group which used the same simulation without scaffolding. Results revealed that the experimental group exhibited significantly greater improvements in scientific understanding and enhanced metacognitive skills in Planning, Monitoring, and Evaluation (PME) compared to the control group. However, no significant differences were observed in other metacognitive dimensions. Notably, the scaffolding intervention proved particularly beneficial for students with lower academic performance, underscoring its potential to support learning in physics simulations. These findings suggest that integrating metacognitive scaffolding into interactive simulations can effectively enhance conceptual understanding and support science learning in elementary education.</p>