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Background: Using simulations in science instruction can help make abstract topics more concrete and boost students' understanding. Aims: The current research examined whether using a simulation as an exploratory learning activity before an accompanying lecture has additional learning and motivational benefits compared to a more common lecture-then-simulation approach. Samples: Participants (Experiment 1, N = 168; Experiment 2, N = 357) were undergraduate students in several sections of a first-year chemistry course. Methods: Students were randomly assigned to explore a simulation on atomic structure either before a lecture (explore-first condition) or after the lecture (instruct-first condition). In Experiment 1, the simulation activity time was limited (15 min) and the activity varied in whether self-explanation (‘why’) prompts were included. In Experiment 2, the activity time was lengthened (20 min), and only ‘why’ prompts were used. After the activity and lecture, students completed a survey and posttest. Results: In Experiment 1, students in the explore-first condition scored lower on posttest conceptual knowledge scores and reported lower curiosity compared to students in the instruct-first condition. Scores for basic facts and transfer knowledge, and self-reported situational interest, self-efficacy, and competence, were equal between conditions. No effects of prompt condition were found. In Experiment 2, with longer activity time, the results reversed. Students in the explore-first condition scored equally on basic facts and higher on conceptual knowledge and transfer measures, while also reporting higher curiosity, situational interest, self-efficacy, competence, and cognitive engagement. Conclusion: When properly designed, placing simulations before—rather than after—lecture can deepen learning, motivation, and competence.