Scaffolding in learning and teacher guidance during inquiry can be attained by formative assessment, which needs to be built into every stage of inquiry. Investigation of the effects of embedded formative assessment in inquiry-based learning on students' conceptual understanding was the aim of this study. Mixed method experimental research design including quantitative and qualitative data collection methods was used for this study. The participants were 41 students, who were in tenth grade of a suburban public high school. The study reached the following conclusions. First, formative assessment combined with inquiry-based teaching serves as a catalyst for students' conceptual learning and elevates effects of inquiry. Second, eliciting evidence of learning and feedback may be the primary stages of formative assessment in accelerating student learning and supporting student knowledge development. This study suggests that assessment should be done when teaching continuous and teachers need to adopt formative assessment while performing inquiry-based teaching.