The purpose of the present explanatory mixed-method design is to examine the effectiveness of a developmental intervention, Embedded Metacognitive Prompts based on Nature of Science (EMPNOS) to teach the nature of science using metacognitive prompts embedded in an inquiry unit. Eighty-three (N = 83) eighth-grade students from four classrooms were randomly assigned to an experimental and a comparison group. All participants were asked to respond to a number of tests (content and nature of science knowledge) and surveys (metacognition and self-regulatory efficacy). Participants were also interviewed. It was hypothesized that the experimental group would outperform the comparison group in all measures. Partial support for the hypotheses was found. Specifically, results showed significant gains in content knowledge and nature of science knowledge of the experimental group over the comparison group. Qualitative findings revealed that students in the comparison group reported scientific thinking in similar terms as the scientific method, while the experimental group reported that scientists were creative and had to explain events using evidence, which is more closely aligned to the aspects of the nature of science. EMPNOS may have implications as a useful classroom tool in guiding students to check their thinking for alignment to the nature of science.