This study explores the effects of metacognitive and cognitive prompting on the scientific inquiry practices of students with various levels of initial metacognition. Two junior high school classes participated in this study. One class, the experimental group (n?=?26), which received an inquiry-based curriculum with a combination of cognitive and metacognitive prompts, was compared to the other class, the comparison group (n?=?25), which received only cognitive prompts in the same curriculum. Data sources included a test of inquiry practices, a questionnaire of metacognition, and worksheets. The results showed that the mixed cognitive and metacognitive prompts had significant impacts on the students' inquiry practices, especially their planning and analyzing abilities. Furthermore, the mixed prompts appeared to have a differential effect on those students with lower level metacognition, who showed significant improvement in their inquiry abilities. A combination of cognitive and metacognitive prompts during an inquiry cycle was found to promote students' inquiry practices.