This study aims to examine the effectiveness of metacognitive scaffolding in different inquiry tasks related to optics. Two high school classes participated in this study. One class, the treatment group (n = 33), which integrated metacognitive prompts into the simulation-based inquiry, was compared to the other class, the control group (n = 34), which received only simulation-based inquiry. Students' conceptual understanding, integrated science process skills, confidence judgment, and inquiry performance were measured using a multiple-choice pretest and post-test and worksheets. The results show that the students' conceptual understanding and confidence judgments on conceptual understanding in both groups significantly increased from the pretest to the post-test. Incorporating metacognitive scaffolds into inquiry-based learning better facilitated the improvement of integrated science process skills as well as the confidence judgment on the process skills, especially in the more complex tasks. The metacognitive scaffolding could be applied to various inquiry activities to enhance students' control of variables, data interpretation, and graph comprehension.