We investigated the effects of just-in-time guidance at various stages of inquiry learning by novice learners. Thirteen participants, randomly assigned to an intervention (n = 8) or control (n = 5) group, were observed as they learned about DC electric circuits using a web-based simulation. Just-in-time instructional prompts to observe, predict, explain, systematically test, collect evidence, and generate rules were strongly associated with diagnosing and correcting misconceptions, and constructing correct scientific concepts. Students' repeated use of predictions, systematic testing, and evidence-coordinated reasoning often led to formulating new principles, generalizing from observed patterns, verifying comprehension, and experiencing "Aha!" moments. Justin-time prompts helped learners manage embedded cognitive challenges in inquiry tasks, achieve a comprehensive understanding of the model represented in the simulation, and show significantly higher knowledge gain. Just-in-time prompts also promoted rejection of incorrect models of inquiry and construction of robust scientific mental models. The results suggest ways of customizing guidance to promote scientific learning within simulation environments.